Molecular diagnostic assay system

ABSTRACT

Improved sub-assemblies and methods of control for use in a diagnostic assay system adapted to receive an assay cartridge are provided herein. Such sub-assemblies include: a brushless DC motor, a door opening/closing mechanism and cartridge loading mechanism, a syringe and valve drive mechanism assembly, a sonication horn, a thermal control device and optical detection/excitation device. Such systems can further include a communications unit configured to wirelessly communicate with a mobile device of a user so as to receive a user input relating to functionality of the system with respect to an assay cartridge received therein and relaying a diagnostic result relating to the assay cartridge to the mobile device.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.15/217,920, filed Jul. 22, 2016 which claims the benefit of priority ofU.S. Provisional Patent Application No. 62/196,845 entitled “MolecularDiagnostic Assay System,” filed on Jul. 24, 2015; the entire contents ofwhich are incorporated herein by reference.

This application is generally related to U.S. patent application Ser.No. 15/217,902, filed Jul. 22, 2016, entitled “Thermal Control Deviceand Methods of Use”; U.S. patent application Ser. No. 15/217,893, filedJul. 22, 2016, entitled “Encoderless Motor with Improved Granularity andMethods of Use” now U.S. Pat. No. 10,348,225; U.S. patent applicationSer. No. 13/843,739 entitled “Honeycomb tube,” filed on Mar. 15, 2013,now U.S. Pat. No. 9,914,968; U.S. patent application Ser. No. 13/828,741entitled “Remote Monitoring of Medical Devices,” filed on Mar. 14, 2013;U.S. Pat. No. 8,048,386 entitled “Fluid Processing and Control,” filedFeb. 25, 2002; and U.S. Pat. No. 6,374,684 entitled “Fluid Control andProcessing System,” filed Aug. 25, 2000; each of which is incorporatedherein by reference in its entirety for all purposes.

BACKGROUND OF THE INVENTION

Technological advancements have made today's world an increasinglyconnected environment. While air travel allows an ordinary person totravel around the globe from one continent to another within one day, itmay also permit rapid spread of contagious pathogens and expose theglobal population to deadly diseases with potentially devastatingconsequences. In the recent past the outbreaks of Severe AcuteRespiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS),and Ebola hemorrhagic fever serve as examples of how a public healthevent that originated in one area on one continent can quickly evolveinto a significant global concern. The highly mobile nature of today'sworld demands reliable diagnostic tools to provide real-time results andto facilitate early detection and immediate response to any potentialepidemics.

On the other hand, there remain many remote and under-developed areas inthis world where health care is not readily available to localresidents. Inadequate accessibility to health care facilities such ashospitals and clinics, or even health product/service retailers (e.g.,drug stores), seriously hinders any effort to achieve timely diagnosisand treatment of patients, especially those suffering from an infectiousdisease, making it difficult to properly assess the risk of an epidemicor to effectively contain an epidemic from rapid spreading. Thus, thereexists a pressing need for new and improved diagnostic tools that arehighly mobile, capable of performing complex molecular testing togenerate rapid, reliable, and accurate diagnostic results, regardless oflocation, whether in a health care facility, neighborhood clinic, retailservice provider, or in a resource-limited setting where electricalpower, communication (e.g., internet), traditional health care servicesand/or health care professionals may not be routinely available.

The present inventors have developed a highly sophisticated yetcompletely portable and surprisingly easy to use molecular diagnosticassay system that fulfills the aforementioned needs. Improved uponexisting molecular diagnostic assay systems (e.g., Cepheid's GeneXpert®system), the new molecular diagnostic assay system described hereinincludes a medical diagnostic device, which is optionally powered bybattery, typically small in size and light in weight, thus permittingcomplete portable use at any location where patients may be, away fromhospitals, laboratories, or even drug stores. The diagnostic device iscapable of performing fully automated molecular diagnostic assays(optionally for detecting multiple pathogens at the same time), rapidlyobtain accurate results (typically within 1 or 2 hours and as fast as15-20 minutes). It is easy to operate, using one or morepre-manufactured assay cartridges one can quickly obtain test resultsindicating whether a patient is carrying particular pathogen(s), orafflicted with a particular disease state.

This newly designed molecular diagnostic assay system also includescomponents that provide secure cloud-based connectivity for conveyingthe diagnostic results from the portable testing device to a remotereporting system, which may be a centralized data collection orprocessing center, or mobile devices such as hand-held devices used by aphysician or a patient to receive a diagnostic report. With suchcloud-supported connectivity, data sharing can take place virtuallyinstantaneously, not only allowing physicians to start treating patientswithout any delay but also enabling monitoring and reporting of anypotential epidemic at a large scale.

These important features circumvent the current limitations that tend toprevent or hinder early diagnosis and effective treatment of patients inpoor, remote areas where health care facilities are few and diagnostictesting capability is scarce. This newly designed molecular diagnosticassay system is the first true point-of-care diagnostic tool possessingthe strength of rapid deployment and full operation in virtually anyenvironment. It truly brings diagnostic testing to people, regardless ofwhere they are. The combination of its deployability, its rapid andaccurate diagnostic functionality, its technical sophistication yet easeof operation, and its cloud-based connectivity makes this new moleculardiagnostic assay system the ultimate solution for the emerging marketsand the revolutionary trend-setter that defines the future of medicaldiagnostic testing.

BRIEF SUMMARY OF THE INVENTION

In one aspect, the invention provides an improved diagnostic assaysystem. Such systems can include improvements pertaining to varioussubassemblies including: a door drive assembly, a syringe drive and avalve drive, a sonication horn, a thermal and optical detectionassembly, and a device management/communication system. It isappreciated that any of these subsassemblies can be included in such adiagnostic assay system separately or in combination with any othersubassembly to provide improved performance aspects as described herein.

In some embodiments, the invention includes a diagnostic assay systemadapted to receive an assay cartridge (also referred to occasionally asa “sample cartridge” or “test cartridge”). Such systems can include anyone or combination of the various features and sub-assemblies describedherein.

In some embodiments, the diagnostic assay system includes a brushless DC(BLDC) motor operatively coupled with, for example, any of a dooropening/closing mechanism and cartridge loading system, a syringe drive,and/or a valve drive.

In some embodiments, the diagnostic assay system includes a dooropening/closing mechanism cooperatively coupled with a cartridge loadingmechanism and driven by a backdriveable transmission mechanism.

In some embodiments, the diagnostic assay system includes a syringedrive operatively coupled with a n-phase BLDC motor and controlled basedat least in-part on monitored current draw of the BLDC motor.

In some embodiments, the diagnostic assay system includes a valve drivemechanism operatively coupled with a n-phase BLDC motor based at leastin-part on a voltage signal provided by n voltage sensors of the BLDCwithout use of any encoder hardware or position sensors.

In some embodiments, the diagnostic assay system includes a sonicationhorn engageable with an assay cartridge for lysing of biologicalmaterial within the assay cartridge and operatively coupled with acontroller configured to control sonication based at least in-part on afrequency providing a highest output amplitude as a resonant frequency.

In some embodiments, the diagnostic assay system includes a thermalcontrol device having a first thermoelectric cooler thermally engageablewith a reaction vessel (also occasionally referred to as a “reactiontube”) of the assay cartridge and at least one other thermalmanipulation device thermally coupled with the first thermoelectriccooler and controlled so as to increase efficiency of the firstthermoelectric cooler to facilitate rapid thermal cycling of thereaction vessel between a first and second temperature with the firstthermoelectric cooler.

In some embodiments, the diagnostic assay system includes an opticalexcitation/detection block mountable relative the reaction vessel so asto emit excitation energy into a fluid sample within the reaction vesselat a substantially orthogonal angle from which excitation is detectedthrough one or more edges (minor face) and/or a major face of thereaction vessel.

In some embodiments, the diagnostic assay system includes acommunications unit configured to wirelessly communicate with a mobiledevice of a user so as to receive a user input relating to functionalityof the system with respect to an assay cartridge received therein andrelaying a diagnostic result relating to the assay cartridge to themobile device.

Some embodiments of the invention relate to a door operating system fora diagnostic assay system. The system can include a chassis of thediagnostic assay system. A brushless DC (BLDC) motor can be coupled tothe chassis of the diagnostic assay system. A back drivable transmissioncan be operable by the BLDC motor. A door can be movable relative to thechassis of the diagnostic assay system from a closed position to an openposition (and from an open position to a closed position). The BLDCmotor can be configured to operate the back drivable transmission basedon current measurements of the BLDC motor, the current measurementsbeing associated with back-driving events against the back drivabletransmission.

Some embodiments of the invention relate to a method for operating adoor opening/closing system for a diagnostic assay system. In themethod, a command can be received to open a cartridge receiving door ofthe diagnostic assay system. A brushless DC (BLDC) motor coupled to aback drivable transmission can be operated to open the door from aclosed position (and vice versa), the back drivable transmission beingoperationally coupled to the door and a cartridge loading mechanism. Afirst back-driving event occurring against the back drivabletransmission can be detected, based on monitoring of the current. Basedon detecting the first back-driving event, operation of the BLDC motorto place the door in an open position can be ceased, and an aspect ofthe cartridge loading mechanism can be placed into position foraccepting an assay cartridge.

Some embodiments of the invention relate to a system for operating asyringe for a diagnostic assay system. The system can include a chassisof a diagnostic assay system. A brushless DC (BLDC) motor can be coupledto the chassis of the diagnostic assay system. A back drivable leadscrew can be operable by the BLDC motor. A plunger rod can be operableby the lead screw to engage a plunger tip in a syringe passage of theassay cartridge. The BLDC motor can be configured to operate the leadscrew based on monitoring current draw of the BLDC motor, the currentbeing associated with pressure changes within the removable assaycartridge.

Some embodiments of the invention relate to a method for operating asyringe for a diagnostic assay system. A command to power a brushless DC(BLDC) motor can be received. The BLDC motor can be operable to turn aback drivable lead screw. A plunger rod can be coupled to and moveableby the lead screw. Power to the BLDC motor can be applied to move theplunger rod to engage a plunger tip within a syringe passage of an assaycartridge. At least one current associated with operation of the BLDCmotor can be monitored to determine a quality of the removable assaycartridge. A change in the current of the BLDC motor can be detected.Operation of the BLDC motor can be altered within the removable assaycartridge based on detecting the change in the current.

Some embodiments of the invention relate to a horn assembly having anultrasonic horn and a horn housing that engages with the disposableassay cartridge through a movable mechanism that moves the ultrasonichorn between a disengaged or retracted position to facilitate loadingand ejection of the assay cartridge from the diagnostic device moduleand an engaged or advanced position to pressingly engage the hornagainst a sonication chamber of the assay cartridge to facilitate lysisof biological cells within the chamber as part of a diagnostic assay,which may include but is not limited to a polymerase chain reactionanalysis. In some embodiments, the movable mechanism includes a springor biasing mechanism and a cam that engages a wedge surface of the hornhousing to effect movement of the horn between the lowered and raisedpositions. In some embodiments, movement of the horn assembly iseffected by an actuator common to other movable components, such as aloading/ejection arm and a cartridge module door so as to provideefficient coordinated movements of components within the diagnosticdevice module.

Some embodiments of the invention relate to a horn having an ultrasonichorn and at least one piezo-electric actuator(s) controlled underclosed-loop feedback. In some embodiments, the horn comprises a controlcircuit that utilizes sinusoidal control and phase matching for controlof resonant frequency. These features ensure in-phase vibration betweenthe piezo-electric actuator(s) so as to provide consistent, robustdelivery of ultrasonic energy with an ultrasonic horn having reducedsize and power requirements than would otherwise be feasible.

Some embodiments of the invention relate to a method for operating avalve drive mechanism. A command can be received to power a brushless DC(BLDC) motor coupled to the chassis to move a valve drive to aparticular position. The valve drive can be configured to rotatepositions of a valve body of a removable assay cartridge. A transmissioncan be coupled between the BLDC motor and the valve drive. The BLDCmotor does not include any positional sensors or encoder hardware, butcan include a plurality of Hall-effect sensors. The BLDC motor can bepowered to rotate a shaft of the BLDC motor a particular number of turnsto move the valve drive to the particular position based on a sinusoidalsignal generated by the Hall-effect sensors.

Some embodiments relate to a system for operating a valve drivemechanism. The system can include a valve drive mechanism chassis. Abrushless DC (BLDC) motor can be coupled to the chassis. The BLDC motordoes not include any positional or encoder hardware, but can include aplurality of Hall-effect sensors. A transmission can be coupled to BLDCmotor. A valve drive can be coupled to the transmission. The valve drivecan be configured to rotate positions of a valve body of a removableassay cartridge. Position of the valve drive output can be determinedbased on analyzing a sinusoidal signal generated by the Hall-effectsensors.

Some embodiments of the invention relate to a diagnostic device whichcan include a Thermal Optical Subassembly (“TOS”) which comprises athermal control device component and an optical excitation/detectcomponent. In some embodiments, the thermal control device includes athermo-electric cooler (“TEC”) component that performs thermal cyclingof a reaction vessel. The optical component excitation/detect componentperforms excitation and optical detection for a target analyte withimproved control, rapidity and efficiency. In some embodiments, the TOSincludes mounting components for interfacing the thermal control devicewith the optical component and defines a cavity for receiving a reactionvessel having a prepared fluid sample for performing an assay for atarget analyte. In some embodiments, the mounting components provide thethermal control device and optical component in proximity to thereaction vessel so as to perform thermal cycling for amplification,excitation and optical detection of the target analyte simultaneously orin rapid succession. In some embodiments, the reaction vessel comprisesa micro-array or a plurality of separate reaction wells and/or apre-amplification chamber within the reaction vessel. In someembodiments, the TOS includes one or more mechanisms that move thethermal control device so as to pressingly engage at least one surfaceof the reaction vessel when positioned within the diagnostic device soas to improve efficiency of thermal cycling. In some embodiments, theTOS is integrated with one or more printed circuit boards (PCB),processors and controllers so as to coordinate thermal cycling andoptical excitation/detection according to a particular assay. In someembodiments, the TOS includes a sensor for detecting proximity of areaction vessel or associated sample assay cartridge to facilitatepositioning of the thermal control device and/or optical componentrelative the reaction vessel or operation thereof.

Some embodiments of the invention relate to a thermal control devicewhich can include a first TEC having an active face and a referenceface; a second TEC having an active face and a reference face; and athermal capacitor or thermal interposer disposed between the first andsecond TECs such that the reference face of the first TEC is thermallycoupled with the active face of the second TEC through the thermalcapacitor. In some embodiments a thermal interposer is positionedbetween the first and second TEC devices. In some embodiments, thethermal interposer acts as a thermal capacitor. In some embodiments, thethermal control device includes a controller operatively coupled to eachof the first and second TECs, the controller configured to operate thesecond TEC concurrent with the first TEC so as to increase the speed andefficiency in operation of the first TEC as a temperature of the activeface of the first TEC changes from an initial temperature to a desiredtarget temperature.

Some embodiments of the invention relate to an optical component thatcan include an optical excitation block and an optical detect blockpositioned on an optical mount that is configured to receive a reactionvessel. In some embodiments, the reaction vessel comprises two opposingmajor planar walls spaced apart from each other by minor planar walls,wherein at least two of the minor planar walls are offset from eachother by about 90 degrees. In some embodiments, the optical excitationblock is positioned to transmit excitation energy into the reactionvessel through one of the minor walls, and the optical detection blockis positioned for detection along a major planar surface of the reactionvessel. In some embodiments, the excitation and detection occurs throughopposing minor walls of the reaction vessel. In some embodiments, theoptical excitation and optical detection components are orthogonal toone other. The optical components are adapted with a relatively lownumerical aperture (e.g. low angular divergence) as compared toconventional systems. Such a configuration provides a larger detectionvolume with lower numerical angles, thereby providing improved opticalsensitivity and facilitating optical alignment.

In another aspect, the TOS includes a sensor for detecting proximityand/or location as well as the identity of an assay cartridge orreaction vessel relative the TOS. In some embodiments, the sensor is anear field communication sensor adapted to detect when an assaycartridge has been loaded into the diagnostic device (also referred tooccasionally as a “diagnostic module”) of the diagnostic assay system,identify the assay, and link the cartridge to a sample identifier. Insome embodiments, the TOS includes a controller for coordinatingoperation of the thermal control device and the optical module inresponse to the sensor.

Some embodiments of the invention relate to a method of managing adiagnostic assay system with a mobile device. At a mobile device, userinput can be received for controlling functionality of a diagnosticdevice. In response to receiving the user input, with the mobile device,control information can be sent to the diagnostic assay device. At themobile device, data (e.g., medical data) can be received from thediagnostic assay device. The data can be relayed to a server withoutstoring or descripting the data.

Some embodiments of the invention relate to a diagnostic assay devicehaving a communications subsystem. The system can include a diagnosticcomponent. A processor communicatively can be coupled with thecommunications subsystem and the diagnostic component. The processor canbe configured to cause the diagnostic assay device to wirelesslyreceive, using the communications subsystem, a device command from amobile device. The processor can also be configured to wirelessly send,using the communications subsystem, a device command response to themobile device. The processor can also be configured to conduct a testusing the diagnostic component. The processor can also be configured towirelessly send, using the communications subsystem, encrypteddiagnostic information (e.g., medical information), indicative of aresult of the test, to a remote server.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is a perspective view of a diagnostic assay system, according tosome embodiments of the invention.

FIG. 1B is an exploded view of a diagnostic assay system, according tosome embodiments of the invention.

FIGS. 2A-2C are perspective views of a brushless DC (BLDC) motor,according to some embodiments of the invention.

FIG. 2D is a graph of a sinusoidal variable voltage output pattern of aBLDC motor, with additional indicia to illustrate a process for encodingthe mechanical angular position of the rotor of the motor according tosome embodiments of the invention.

FIG. 2E is a circuit diagram for controlling a BLDC motor, according tosome embodiments of the invention.

FIGS. 3A-3C are diagrams of models for determining torque output of aBLDC motor, according to some embodiments of the invention.

FIG. 4A is a perspective view of a door opening mechanism, according tosome embodiments of the invention.

FIGS. 4B-4E are cross sectional views of a diagnostic assay system inuse, according to some embodiments of the invention.

FIG. 5A is a cross sectional view of a diagnostic assay system in use,according to some embodiments of the invention.

FIGS. 5B and 5C are flow diagrams of a method for operating aspects of adiagnostic assay system, according to some embodiments of the invention.

FIGS. 6A and 6B are perspective views of a valve drive mechanism,according to some embodiments of the invention.

FIG. 6C is a graph relating an output signal to valve drive position,according to some embodiments of the invention.

FIGS. 7A-B illustrates an ultrasonic horn assembly for use in diagnosticassay system in accordance with some embodiments of the invention.

FIGS. 8A-D illustrates component views of ultrasonic horn assembly inaccordance with some embodiments of the invention.

FIGS. 9A-B illustrates cross-sectional views of a diagnostic assaysystem during and after loading of an assay cartridge in accordance withsome embodiments of the invention.

FIG. 10A illustrates cross-sectional view of an assay cartridge and FIG.10B illustrates a cut-away view of an assay cartridge loaded in adiagnostic assay system with an ultrasonic horn assembly in accordancewith some embodiments of the invention.

FIGS. 11A1-2 to 11B1-2 illustrates side and cross-section views of ahorn assembly in a disengaged position and a engaged position,respectively, in accordance with some embodiments of the invention.

FIG. 12A illustrates an examplary ultrasonic horn and FIG. 12Billustrates a control diagram for operation of an ultrasonic horn inaccordance with some embodiments of the invention.

FIG. 13 illustrates a transfer function for control of a horn assemblyin accordance with some embodiments of the invention.

FIG. 14 illustrates a control schematic of a horn assembly in accordancewith some embodiments of the invention.

FIG. 15-17 illustrate control diagrams for a horn assembly in accordancewith some embodiments of the invention.

FIG. 18 illustrates an exemplary TOS sub-assembly before insertion intothe assay module in accordance with some embodiments of the invention.

FIGS. 19A-19B illustrates front and rear views of an exemplary TOSsub-assembly in accordance with some embodiments of the invention.

FIGS. 20A-20B illustrates exploded views of an exemplary TOS inaccordance with some embodiments of the invention.

FIGS. 21A-B illustrates optical components and associated PCBs of anexemplary TOS in accordance with some embodiments of the invention.

FIGS. 22A-B illustrates exemplary thermal control device components andassociated PCB with a rigid flex connection in an example TOS inaccordance with some embodiments of the invention.

FIGS. 23A-B illustrates an exemplary thermal control device componentconfigured to interface with an optical mount of an example TOS inaccordance with some embodiments of the invention.

FIGS. 24A-B illustrate an exemplary thermal control device componentmovably coupled to an optical mount in an openconfiguration and aclamped configuration, respectively, in accordance with some embodimentsof the invention.

FIG. 25 illustrates an exemplary thermal control device componentmovably coupled to an optical mount and a slide base in accordance withsome embodiments of the invention.

FIGS. 26A-B illustrates an exemplary thermal control device componentmovably coupled with a slide base actuated by a door rack of the modulein accordance with some embodiments of the invention.

FIG. 27 illustrates an exemplary block control diagram of components ofthe TOS in accordance with some embodiments of the invention.

FIG. 28 illustrates an exemplary schematic of optical and thermalcontrol components of the TOS in accordance with some embodiments of theinvention.

FIG. 29 illustrates an exemplary TOS for use in a diagnostic assaysystem in accordance with some embodiments of the invention.

FIGS. 30A-B illustrate two exemplary optical component configurationsfor use with a reaction vessel in a diagnostic device in accordance withsome embodiments of the invention and FIG. 30C illustrates a detailedschematic of an exemplary optical component configuration in accordancewith some embodiments of the invention.

FIG. 31 illustrates exemplary detailed views of the excitation block 310and the detection block 320 in accordance with some embodiments of theinvention.

FIG. 32 illustrates fluorescence detection with the excitation anddetection components of an exemplary optical component in accordancewith some embodiments of the invention.

FIG. 33A illustrates a schematic of a thermal control device inaccordance with some embodiments of the invention.

FIGS. 33B-C illustrates models of an exemplary thermal control device inaccordance with some embodiments of the invention.

FIG. 34 shows a thermal cycle under closed loop control in accordancewith some embodiments of the invention.

FIG. 35 shows ten successive thermal cycles over a full range of PCRthermo-cycling in accordance with some embodiments of the invention.

FIG. 36A shows thermo-cycling performance for five cycles at thebeginning of thermal cycling and after two days of continuous thermalcycling.

FIG. 36B shows a control diagram of set points used in control loops inaccordance with some embodiments of the invention

FIG. 37 shows a diagram of set points used in control loops inaccordance with some embodiments of the invention.

FIG. 38 is an exemplary illustration of the software architecture of adiagnostic assay system according to some embodiments of the invention.

FIG. 39 provides a logical view of software executed by the diagnosticdevice, according to some embodiments of the invention.

FIG. 40 is a block diagram of the diagnostic assay system (EpsilonInstrument Core Architecture), according to some embodiments of theinvention.

FIGS. 41-1 through 41-4 are diagrams illustrating various states of theHierarchical System Machine (HSM) component, according to someembodiments of the invention.

FIG. 42 is a diagram illustrating instrument core internal componentsand interfaces, according to some embodiments of the invention.

FIG. 43 is a block diagram illustrating software components executed ona mobile device, according to some embodiments of the invention.

FIG. 44 is a block diagram illustrating software components executed bya remote diagnostics reporting service, according to some embodiments ofthe invention.

FIG. 45 is a data flow diagram illustrating top level data flow in adiagnostic assay system, according to some embodiments of the invention.

FIG. 46 is a data flow diagram illustrating an embodiment of a moredetailed data flow than FIG. 45 , in which components of the mobiledevice are separately portrayed.

FIG. 47 is a data flow diagram illustrating the process for a locationconfiguration of a diagnostic assay system, according to someembodiments of the invention.

FIG. 48 is a data flow diagram illustrating the process for providingoperational updates to a mobile device in a diagnostic assay system,according to some embodiments of the invention.

FIG. 49 is a data flow diagram illustrating the process for providingoperational updates to a diagnostic device in a diagnostic assay system,according to some embodiments of the invention.

FIG. 50 is a data flow diagram of such a process in a diagnostic assaysystem, according to some embodiments of the invention.

FIG. 51 is a data flow diagram illustrating the process for providingdiagnostic device commands in a diagnostic assay system, according tosome embodiments of the invention.

FIG. 52 is a data flow diagram illustrating the process for providingmedical diagnostic device registration on a network of a diagnosticassay system, according to some embodiments of the invention.

FIG. 53 is an illustration of a computer system, according to someembodiments of the invention, which can be incorporated, at least inpart, into devices and components of the diagnostic assay systemdescribed herein.

FIG. 54 is a flow diagram of a method of managing a diagnostic assaysystem with a mobile device, according to some embodiments of theinvention.

DETAILED DESCRIPTION OF THE INVENTION

I. System Overview

FIG. 1A shows a perspective view of a system 10 for testing a biologicalsample, according to embodiments of the invention. The compact formfactor of the system 10 provides a portable sample testing device thatcan communicate wirelessly or directly (wired) with a local computer orcloud-based network. As such, the system 10 can be advantageously usedfor point-of-care applications including mobile diagnostic centers, inemerging countries, and in physician office labs.

The system 10 is usable with a disposable assay cartridge, which isconfigured to accept a biological sample and adapted for performing aparticular assay. The system and cartridges are highly flexible and canbe used to detect a variety of analytes, including nucleic acid andprotein. Non-limiting exemplary analytes that can be detected using thesystem and assay cartridges includes, bacteria, viruses, and diseasespecific markers for a variety of pathogenic disease states includingHealth Associated Infections (MRSA, C. Difficile, Vancomycin resistantenterococcus (VRE), Norovirus), Critical Infectious Diseases (MTB/RIF,Flu, RSV, EV), Sexual Health (CT/NG, GBS), oncology (e.g., breast orbladder cancer) and Genetics (FII/FV). In some embodiments, the system10 can identify the type of cartridge via integrated near fieldcommunication ability (e.g. RFID, laser scanning), and thus apply theappropriate assay routine to the cartridge. In some embodiments,cartridge identification uses Bluetooth technology, RFID tags,barcoding, QR labels, and the like.

Once a assay cartridge is physically inserted within and initialized bythe system 10, the system will perform the functions of specimenprocessing, which can in some embodiments include sample preparation,nucleic acid amplification, and an analyte detection process. Results ofthe detection process can be uploaded wirelessly or directly by wire toa local computer or cloud based network. Advantageously, the localcomputer can be a wireless communication device, such as a tablet orcellular phone, having a software application specifically designed tocontrol the system and communicate with a network.

The system 10 can be powered by an external power source, but canfeature an uninterruptable power supply (e.g. batteries) in case ofpower disruption or field use. The uninterruptable power supply (UPS)allows for field use of the system, and in some embodiments can providepower to the system for at least one day, preferably up to two days. Insome embodiments, the UPS allows for up to four hours of continuousoperation. As shown in this external view, the system 10 can include anouter shell 12 and a door 14 for accepting an assay cartridge (notshown). Different styles of the outer shell 12 can be configured asneeded by a particular user. Typically, outer shell 12 is formed of asubstantially rigid material so as to protect and support the componentswithin, for example, a hardened polymer or metal construction. Althoughnot shown here, in some embodiments the outer shell 12 can be heavilyruggedized (armored) for field use, or as shown here made decorative forphysician office use.

FIG. 1B shows an exploded view of the system 10 (without the outershell) and with major subsystems depicted outwardly. An overview of thesubsystems is provided below. Additional details of each subsystem aredescribed in the following sections.

Various sub-systems are disclosed that make use of brushless DC (BLDC)motors. Generally, each motor can have a stator assembly that is mountedto a printed circuit board (PCB) substrate, and can include a backdrivable transmission mechanism, such as a lead screw. In someembodiments, such BLDC motors make use of analog sensors (e.g.,Hall-sensors) for determining angular positioning and force-basedcurrent monitoring as a triggering tool. Such BLDC motors can include arotor with multiple magnets disposed thereon and mounted to a stator ona substrate with at least as many sensors as phases of the motor. Thethree sensors are positioned such that the displacement of the rotor canbe controlled based on the linear portions of measurements from thesensors, thereby providing improved resolution and granularity withoutrequiring use of any position-based sensors or encoder hardware. Thus,the BLDC motors described herein do not require use of encoder hardwareand their associated drive trains do not require use of positionsensors. For example, the system can include a syringe drive mechanism16 that includes a brushless BLDC motor having an output shaft that ismated to a back drivable lead screw. The lead screw drives a plunger rodthat can interface with a plunger tip of a removable assay cartridge.Such a syringe drive mechanism 16 can share a PCB 30 with a door drivemechanism 18. The door drive mechanism also includes a BLDC motor havingan output shaft that is mated to a back drivable lead screw. The motorsof the syringe drive mechanism 16 and door drive mechanism 18 are showndirectly mounted to opposite sides of a PCB board, however, this is notcritical and both motors can be mounted to the same side. In someembodiments, each motor can be mounted to its own PCB. It isadvantageous to utilize such BLDC motors as the improved resolution andgranularity allows for improved accuracy and efficiency, and furtherallows for further miniaturization of mechanisms driven by such motors.It is appreciated, however, that use of such BLDC motors is not requiredand that any of the mechanisms described herein could also be driven byconventional type motors if desired, but additional sensors and/orcircuitry may be required for some embodiments.

As mentioned above, the BLDC motor is unique in that includes aplurality of Hall-effect sensors, but does not include any traditionalencoder hardware. In some embodiments, the syringe drive mechanism anddoor drive mechanism, and associated subsystems, do not include positionsensors. In some embodiments, the angular position of the rotor andoutput shaft of the BLDC can be solely derived from the sinusoidal waveoutput of the analog sensors and the circuitry on the PCB. Thus,traditional position sensors (e.g. encoders, optical sensors, etc.) arenot required for use in conjunction with the BLDC motors as used in theinstant invention. In order for the BLDC motor to provide smooth torqueproduction, motor control techniques such as sine-wave commutation canbe implemented. Further, pulse-width modulation implementation can beused to center the drive voltages to achieve high speed operation.

In addition, because the lead screws of the mechanisms are backdrivable, force-based end-of-travel detection can be used to determinestart and stop points for driving the mechanisms. Force-basedend-of-travel detection can be derived by monitoring the current of theBLDC motors, e.g., the current of a bridge circuit, which will deviate(increase or decrease) from a norm when a force-based event occurs.Hence, this deviation can be used as a trigger event to start, stop,reverse, slow down, and/or speed up a BLDC motor. For example, in thecase of the syringe drive mechanism 16, current sensing can becorrelated to pressure, and thus be used to deliver a consistent orintentionally varying pressure to the plunger rod by tuning the RPM ofthe associated BLDC motor. This alleviates the need for an in-linepressure sensor to monitor cartridge pressure.

Valve drive mechanism 20 can make similar use of the same type of BLDCmotor. In some embodiments, the valve drive mechanism 20 can include aworm drive gear train, which ultimately outputs to a turntable likevalve drive for rotating the valve of a removable assay cartridge. Insome embodiments, the worm drive mechanism is not back drivable as inthe aforementioned syringe drive and door drive mechanisms. However, thesame type of Hall-effect position determination and force basetriggering (current monitoring) can be used for the valve drivemechanism. For example, if turning the valve drive unexpectedly requiressubstantially less or more current, then such an event can be indicativeof a jam or failure of an assay cartridge. Here, force base triggeringcan be used to sense a cartridge integrity malfunction.

Sonication horn mechanism 22 is partially integrated with the valvedrive mechanism 20. The sonication horn mechanism 22 can apply aprogrammable sonication power for a programmable duration to thecartridge, for example, in order to lyse a target sample within thecartridge. In some embodiments, the sonication horn mechanism 22 canemploy a resonant piezo-electric actuator to apply vibration at afrequency of about 30 kHz or greater, about 40 kHz or greater, such asabout 50 kHz (e.g. 50.5 kHz). The sonication horn mechanism 22 includesa control circuit that uses the phase of measured current in relation tothe voltage excitation to determine the resonant frequency. Thefrequency can be adjusted by the control circuit to maintain a presetphase relationship. In some embodiments, the amplitude of the voltageexcitation can be continually adjusted to maintain the commanded powerlevel. Based on these functions, the control circuit can maximize poweroutput of the horn.

The system 10 also includes a door drive and cartridge loading system 24that is powered by the door drive mechanism 18. The lead screw of thedoor drive mechanism 18 outputs power to the door drive and cartridgeloading system 24 to both open and close the door 14 as well as engageand intake an assay cartridge 32.

A rear chassis portion 26 and a front chassis portion 28 providestructural support for the system 10, as well as mounting provisions forthe other subsystems. The chassis portions are generally elongated toprovide a smaller overall footprint for the system 10, and enableportability of the system 10. In some embodiments, the system can have afoot print of: 9.1″×3.0″×4.2″, and an approximate weight of 2.2 lbs. Theelongated circuit board or PCB 30 generally matches the foot print ofthe chassis portions. The PCB 30 includes most or all of the processors,sub-processors, memory, and control circuits required to control thesystem 10. However, the aforementioned BLDC motors can be integratedwith their own respective printed circuit boards that have controlcircuits that connect separately to the PCB 30. The PCB 30 also includescommunication circuit aspects (e.g. near field communication circuits,USB, wireless) as well as a power supply circuit.

The system 10 is compatible with various types of assay cartridges 32,which are generally configured for receiving and holding a sample ofmaterial, such as a bodily fluid (e.g., blood, urine, salvia) or solid(e.g., soil, spores, chemical residue) that is liquid soluble. The assaycartridge 32 can be a walled structure having one or more fluid channelsand connection ports. The assay cartridge 32 may be relatively small,such that it can easily be hand-held, portable, and/or disposable.Examples of such cartridges (useable with the system 10) are disclosedin U.S. Pat. No. 6,660,228, Int'l Pub. No. WO 2014052671 A1, U.S. Pat.No. 6,374,684, which are each incorporated by reference herein for allpurposes.

The assay cartridge 32 can include a reaction vessel 33 extendingoutward from the rear, which interfaces with a thermal cycling anddetection module 34. The module 34 includes one or more apparatusesconfigured to deliver energy to, and also remove energy from, an aspectof the assay cartridge 32. Such an apparatus can include a dualthermoelectric cooler. The module 34 also includes one or more detectionaspects, as discussed in further detail below.

II. Brushless DC (BLDC) Motor Architecture

FIG. 2A is a plan view diagram illustrating elements of a brushless DC(BLDC) motor 100, for use with some embodiments of the invention.Further details of the BLDC motor can be found at commonly assigned U.S.Provisional Application No. 62/195,449, filed Jul. 22, 2015, andentitled “Simple Centroid Implementation of Commutation and Encoding forDC Motor,” which is hereby incorporated by reference for all purposes.

In one aspect, the BLDC motor includes a rotor and stator configured toproduce a smoothly varying Hall-effect voltage without any need forfiltering or noise reduction. In some embodiments, this feature isprovided by use of permanent magnets within the rotor that extend adistance beyond the magnetic core of the stator. In some embodiments,the BLDC motor includes as many Hall-effect sensors as phases of themotor, which are positioned such that the motor can be controlled basedon substantially only the linear portion of the measured voltagepatterns received from the sensors. In some embodiments, this includesspacing the sensors radially about the stator such that the linearportions of the measured voltage waveforms intersect. For example, athree-phase BLDC can include three Hall-effect sensors spaced 40 degreesradially from each other, thereby allowing the system to control aposition of the sensor within an increment of 40 degrees.

In some embodiments, the motor comprises an internal stator assembly 101having nine pole teeth extending radially from center, each pole toothending in a pole shoe 103, and each pole tooth having a windingproviding an electromagnetic coil 102. The motor further comprises anexternal rotor 104 having an external cylindrical skirt 105 and twelvepermanent magnets 106 arranged with alternating polarity around theinner periphery of the skirt 105. The permanent magnets are shaped toprovide a cylindrical inner surface for the rotor with close proximityto outer curved surfaces of the pole shoes. The BLDC motor in thisexample is a three-phase, twelve pole motor. Controls provided, but notshown in FIG. 2A, switch current in the coils 102 providingelectromagnetic interaction with permanent magnets 106 to drive therotor, as is well-known in the art.

It should be noted that the number of pole teeth and poles, and indeedthe disclosure of an internal stator and an external rotor areexemplary, and not limiting in the invention, which is operable withmotors of a variety of different designs.

FIG. 2B is a side elevation view, partly in section, of the motor ofFIG. 2A, cut away to show one pole tooth and coil of the nine, ending inpole shoe 103 in close proximity to one of the twelve permanent magnets106 arranged around the inner periphery of cylindrical skirt 105 ofexternal rotor 104. The pole teeth and pole shoes of stator assembly 101are a part of the core, and define a distal extremity of the core at theheight of line 204. Stator assembly 101 is supported in thisimplementation on a substrate 201, which in some embodiments is aprinted circuit board (PCB), which PCB can comprise controls and tracesfor managing switching of electrical current to coils 102, providingelectromagnetic fields interacting with the fields of permanent magnets106 to drive the rotor. The PCB as substrate can also comprise controlcircuitry for encoding and commutation. Rotor 104 engages physicallywith stator 101 by drive shaft 107, which engages a bearing assembly inthe stator to guide the rotor with precision in rotation. Drive shaft107 in this implementation passes through an opening for the purpose inPCB 107, and can be engaged to drive mechanical devices.

Three linear Hall-effect sensors 202 a, 202 b, and 202 c are illustratedin FIG. 2B, supported by substrate 201, and positioned strategicallyaccording to some embodiments of the invention to produce a variablevoltage pattern that can be used in a process to encode angular positionof the rotor and provide commutation for motor 100. In FIG. 2B theoverall height of skirt 105 of rotor 104 is represented by dimension D.Dimension d1 represents extension of the distal extremity of the rotormagnets below the distal extremity of the core at line 204. Inconventional motors there is no reason or motivation to extend this edgebelow the extremity of the core, particularly since this can increasethe height of the motor and require increased clearance between therotor and substrate. In fact, the skilled artisan would limit dimensionD so there is no such extension, as the added dimension would only addunnecessary cost and bulk to a conventional motor. Furthermore, inconventional motors at the distal extremity of the rotor, at the heightof or above the distal extremity of the core, switching of current incoils 102 creates a considerable field effect, and a signal detected bya Hall-effect sensor placed to sense permanent magnets at that positionwould not produce a smoothly varying Hall-effect voltage. Rather, theeffect in a conventional motor is substantially noise corrupted. Theconventional approach to this dilemma is to introduce noise-filtering,or more commonly to utilize an encoder.

Extending the rotor magnets below the distal extremity of the iron coreavoids the corrupting effect of the switching fields from the coils ofthe stator on the signal detected by the Hall-effect sensors. Theparticular extension d1 will depend on several factors specific to theparticular motor arrangement, and in some embodiments will be 1 mm ormore (e.g. 2 mm, 3 mm, 4 mm, 5 mm, 6 mm, or greater), while in someembodiments the extension will be less than 1 mm. In some embodiments,the distance is a function of the size of the permanent magnets and/orthe strength of the magnetic field. In some embodiments, as detailedherein, 1 mm of extension is sufficient to produce a sinusoidal signalof varying voltage without noise or saturation. Placement of theHall-effect sensors at a separation d2 to produce a Hall-effect voltageproduces a smoothly variable voltage, devoid of noise. In someembodiments, the Hall-effect sensors produce a smoothly variable DCvoltage in the range from about 2 volts to about 5 volts devoid of noiseor saturation. The dimension d2 may vary depending on choice of sensor,design of a rotor, strength of permanent magnets in the rotor, and otherfactors that are well known to persons of skill in the art. A workableseparation is readily discovered for any particular circumstance, toavoid saturation of the sensor and to produce a smoothly variable DCvoltage substantially devoid of noise.

FIG. 2C is a plan diagram of a portion of substrate 201 taken in thedirection of arrow 3 of FIG. 2B, showing placement of Hall-effectsensors 202 a, 202 b, and 202 c relative to the distal edge of rotor104, which may be seen in FIG. 2B to extend below the distal edge of thecore by dimension d1. In FIG. 2C the rotation track of rotor 104including the twelve permanent magnets 106 is shown in dotted outline302. The rotor rotates in either direction 303 depending on details ofcommutation.

As illustrated in this non-limiting exemplary embodiment, each ofHall-effect sensors 202 a, 202 b, and 202 c is positioned radiallybeneath the distal edge of the rotor magnets, just toward the inside ofthe central track of the rotating magnets. Hall-effect sensor 202 b islocated forty degrees arc from Hall-effect sensor 202 a along therotating track of the magnets of the rotor. Similarly, Hall-effectsensor 202 c is located a further forty degrees around the rotor trackfrom Hall-effect sensor 202 b.

FIG. 2D illustrates three voltage patterns 401, 501 and 601 produced bypassage of permanent magnets 106 of rotor 104 over Hall-effect sensors202 a, 202 b, and 202 c in a three-phase BLDC motor. A sinusoidalvariable voltage pattern 401 produced by passage of permanent magnets106 of rotor 104 over Hall-effect sensor 202 a. The 0 degree startingpoint is arbitrarily set to be at a maximum voltage point. Threecomplete sine waveforms are produced in one full 360 degree revolutionof the rotor. Voltage pattern 501 produced by passage of permanentmagnets 106 of rotor 104 over Hall-effect sensor 202 b. Further, asubstantially noise free sinusoidal variable voltage pattern 501produced by passage of permanent magnets 106 of rotor 104 overHall-effect sensor 202 b. As Hall-effect sensor 202 b is positioned atan arc length of 40 degrees from the position of Hall-effect sensor 202a, sinusoidal pattern 501 is phase-shifted by 120 degrees from that ofsinusoidal pattern 401. Yet further, a substantially noise freesinusoidal variable voltage pattern 601 produced by passage of permanentmagnets 106 of rotor 104 over Hall-effect sensor 202 c. As Hall-effectsensor 202 c is positioned at an arc length of 40 degrees from theposition of Hall-effect sensor 202 b, sinusoidal pattern 601 isphase-shifted by 120 degrees from that of sinusoidal pattern 501. Thepatterns repeat for each 360 degree rotation of the rotor.

The three voltage patterns 401, 501 and 601 each have substantially thesame max and min peaks, as the Hall-effect sensors are identical, andare sensing the same magnetic fringe fields at the same distances.Moreover, patterns 401, 501 and 601 intersect at multiple points, points402, 502, and 602 being examples. Notably, the pattern segments betweenintersection points are substantially straight lines, and may be seen toprovide an endless, continuing sequence of connected straight-linesegments. Further, zero-crossing points for each straight line segment,and max and min peaks for each pattern may be sensed and recorded.

FIG. 2D further illustrates two straight line segments between crossingpoints 402, 502, and 602. As a non-limiting example, the segment betweencrossing points 402 and 502 is shown divided into 20 equal-lengthsegments, which may conveniently be done by sensing the voltage atcrossing points 402 and 502, and simple division. Because the physicalrotation of the rotor, in this example, from one pattern intersection toanother is twenty degrees of motor rotation, each voltage change by thecalculated amount then represents 20/20, that is, 1.00 degrees ofrotation of the rotor. This is a relatively gross example to merelyillustrate the method. In some embodiments of the invention, circuitryon PCB 201 senses the crossing points and divides by an 11-bit analog todigital converter (ADC) between the intersections. This provides 2048counts. In this implementation the mechanical rotational translation ofrotor 205 for each count is about 0.0098 degree. Resolution of thesystem can be increased (or decreased) by using an ADC with a higher (orlower) bit resolution. For example, using an 8-bit ADC would resolveeach count to about 0.078 degrees, a 16-bit ADC would resolve each countto 0.00031 degrees, and using a 20-bit ADC would resolve each count toabout 0.00002 degrees. Alternatively, increasing or decreasing thenumber of poles will correspondingly increase or decrease the resolutionof the system.

In some embodiments, the invention provides for a high degree ofaccuracy and precision for mechanisms driven by motor 100. In thenon-limiting example described above using an 11-bit ADC, the motorposition can be controlled to 0.0098 degree mechanical. Coupled withgear reduction extremely fine control of translation and rotation ofmechanisms can be attained. In some embodiments, motor 100 is coupled toa translation drive for a syringe-pump unit to take in and expel fluidin diagnostic processes.

FIG. 2E is a diagram depicting circuitry in some embodiments of theinvention for controlling motor 100 using the output of the Hall-effectsensors and the unique method of analyzing only the linear portions ofphase-separated curves produced by the sensors, the linear portionsdivided into equal segments divided as described above. Output of theHall-effect sensors 202 a, 202 b, and 202 c is provided to aproportional-integral-derivative (PID) motion control circuitry forcommutation purpose, and the waveforms produced by interaction of therotor magnets with the Hall-effect sensors is provided to multiplexercircuitry as shown in FIG. 2E. As described above in the non-limitingexemplary embodiments, an ADC is used to produce the division of thestraight portions of the phase-separated waveforms and motor 100, whichcan be driven by, for example, a DRV8313 Texas Instruments motor drivercircuit. The skilled person will understand the circuitry is notnecessarily unique, and will understand further that there are otherarrangements of circuitry that might be used while still falling withinthe scope of the instant invention. In some embodiments the circuitryand coded instructions for sensing the Hall-effect sensors and providingmotor encoding can be implemented in a programmable system on a chip(PSoC) on the PCB. The circuitry can also include a torque estimatingcircuit, which can be provided to estimate torque values generated bythe motor based on current and voltage measurements taken at the PSoC,thus avoiding the need for additional force sensors throughout thegreater system.

III. Motor Torque Estimation

In some embodiments, aspects of the BLDC motor 100 and control circuitscan be used to detect torque without the need for extraneous sensors.This can be accomplished in different ways, for example by estimatingtorque based on the principle that the electrical power put forth intothe BLDC motor is equal to the mechanical power extracted from the motorin addition to the electrical power dissipated by the motor (i.e. copperloss), as illustrated by the model shown at FIG. 3A. This principal isquantified by the following equation:P _(in) =P _(out) +P _(CL)

Where dissipated power P_(CL) is calculated from:

$P_{CL} = {\frac{3}{2}i_{q}^{2}r_{m}}$${P_{CL} = {{\frac{3}{2}\frac{r_{m}}{K_{t}^{2}}\tau_{m}^{2}\mspace{14mu}{or}\mspace{14mu} P_{CL}} = {\alpha_{CL}\mspace{14mu}\tau_{m}^{2}}}},{{{with}\mspace{14mu}\alpha_{CL}} = {\frac{3}{2}\frac{r_{m}}{K_{t}^{2}}}}$

Referring to the power balancing equation above, it logically followsthat:0=P _(out) +P _(CL) −P _(in)

Substitution of the power variables results in the following balancedequation:0=(α_(CL)*τ_(m) ²)+(ω_(m)*τ_(m))−(v _(B) *i _(B))

Hence, solving for the motor torque τ_(m), the following equationresults:

$\tau_{m} = \frac{{- \omega_{m}} \pm \sqrt{\omega_{m}^{2} - {4\alpha_{CL}v_{B}i_{B}}}}{2\alpha_{CL}}$

It follows that here are two possible calculated solutions for the motortorque, which are the most positive and most negative torque solutionsgenerated by the preceding equation, using bridge current i_(B), asshown below:

${\hat{\tau}}_{m\; 1} = {{\frac{{- \omega_{m}} + \sqrt{\omega_{m}^{2} - {4\alpha_{CL}v_{B}i_{B}}}}{2\alpha_{CL}}\mspace{14mu}{and}\mspace{14mu}{\hat{\tau}}_{m\; 2}} = \frac{{- \omega_{m}} - \sqrt{\omega_{m}^{2} - {4\alpha_{CL}v_{B}i_{B}}}}{2\alpha_{CL}}}$

Given that torque is calculable from the motor constant and othervariables, the motor torque can also be calculated using the motorconstant K_(t), as depicted at the motor models as shown at FIGS. 3B and3C.

${{\hat{\tau}}_{m} = {{K_{t}\mspace{14mu} i_{q}} \cong {K_{t}\frac{v_{q} - v_{EMF}}{\frac{3}{2}r_{m}}}}},{{{where}\mspace{14mu} V_{EMF}} = {K_{t}\omega_{m}}}$

Thus, the calculated solution {circumflex over (τ)}_(m1) or {circumflexover (τ)}_(m2) that is closest to the calculation for {circumflex over(τ)}_(m) (using K_(t)) is assumed to be the correct solution. Thefollowing table defines the variables above.

Variable Notation Details Bridge Voltage ν_(b) The DC bus voltagesupplied to the motor drive power electronics Bridge Current i_(b) Thecurrent supplied to the motor drive power electronics by the bus voltageLow-pass filter f_(B) The bandwidth in Hz of the low-pass bandwidthfilters employed in the force computation Discrete Time T_(s) Theinterval between the samples in the Sample Period discrete time controlsystem. Motor Torque τ_(m) The motor torque applied to the rotor by thestator windings Motor Velocity ω_(m) The angular velocity of the motorMotor Torque {circumflex over (τ)}_(m) ₁ , {circumflex over (τ)}_(m) ₂The most positive and most negative solutions torque solutions generatedby the Motor Torque Solution Algorithm q, d ( )_(q), ( )_(d) Thecomponent of voltage or current that components aligns with thetorque-producing, q, and non-torque-producing, d, vectors that denotethe q,d coordinate system. Motor ω_(e) The motor electrical frequency-avalue Electrical equal to the product of the number of Frequencypole-pairs, N_(p)/2 and the motor angular velocity, ω_(m) Motor Constantk_(t) The motor constant that determines the scaling relationshipbetween the motor torque and motor current (τ_(m) = k_(t)i_(q)) andbetween the motor voltage and motor angular velocity (ν_(q) =k_(t)ω_(m)). Motor voltage ν_(q), ν_(d) The vector that defines themotor voltage within the (q,d) coordinate system Motor current i_(q),i_(d) The vector that defines the motor current within the (q,d)coordinate system Motor Winding V_(A), V_(B), V_(C) The voltages appliedby the three-phase Voltage inverter to the motor windings EMF Voltageν_(emf) The back-emf (electro-motive force) is the open-circuit voltagegenerated when rotating the motor rotor, ν_(emf) = k_(t)ω_(m) Estimatedor {circumflex over (()}^{circumflex over ())} This refers to thecomputed value, computed including filtered signal representations.value Lack of the “hat” designation refers to the actual value prior tosensing. Motor r_(m) This is the winding resistance as resistancemeasured from output to “center tap.”

The principles above can be relied on for estimating torque values basedon the readily available current and voltages measurements, which isachievable using a low-cost Programmable System-on-Chip integratedcircuit, such as the PSoC® line of circuits available from CyprusSemiconductor Corp. Additional variables such as friction can beaccounted for, as well as cogging effects that arise from harmonicdisturbance torques by using a Kalman filter for example. As one ofordinary skill in the art would understand, the advantage of using alow-cost and simple integrated circuit for torque estimation provides agreat advantage over prior devices that rely on sensors (pressuresensors, encoders, etc.) for providing device feedback, thus reducingthe number of parts required and cost of the system as a whole. Thisadvantage is greatly realized when torque sensing is used for triggeringcommands, as depicted in the Door Opening and Cartridge Loading, SyringeDrive, and Valve Drive sub-systems described below.

IV. Door Opening and Cartridge Loading Sub-System

In another aspect, the invention provides a door opening/closing andcartridge loading sub-system that is driven by a backdriveable mechanismso as to facilitate ease in manual loading and unloading an assaycartridge from the diagnostic assay system. In some embodiments, thedoor opening/closing mechanism and cartridge loading system areintegrated so as to provide coordinated movement such that manualloading of the cartridge into an open bay of the system initiatesclosing of the bay door, typically upon detection of backdriving of themechanism as the user manually pushes the cartridge into the system. Itis appreciated that such mechanisms can be driven by a BLDC motor, asdescribed herein, and utilize motor torque estimation, or utilizevarious conventional motors and approaches as would be known to one ofskill in the art. Examples of such configurations are detailed below.

FIG. 4A shows a perspective view of a door opening and cartridge loadingsub-system 1400. The system includes a brushless DC (BLDC) motor 100, asdescribed above, mounted to a PCB 30′. The BLDC motor 100 includes anoutput shaft (not shown) to which a lead screw 109 is attached. The leadscrew 109 is back drivable aspect of a transmission that operates toopen and close the door 14 as well as power a cartridge loadingmechanism.

The lead screw 109 is threadingly engaged with a nut of a bridge 108,hence, when the lead screw 109 turns, the bridge 108 moves upward ordownward (as the device is oriented in FIG. 4A) depending on thedirection the lead screw 109 turns. A first rack portion 110 and asecond rack portion 112 are affixed to the bridge 108. Both rackportions are elongated to include a rack 114 and a cam pathway 116, thatforms an “L” like path.

A pair of pinion gears 118 are meshed with the racks 114. Up and downmovement of the racks 114 is caused by movement of the bridge 108 andthe lead screw 109, which causes the pinions 118 to rotate accordingly.The pinion gears 118 are connected to each other by a shared shaft 120that is supported by a sub-frame 122, which is affixed to a greaterportion of the system 10, such as rear chassis portion 26. Each piniongear 118 includes a finger 124 for stopping rotation of the pinion gear118 at certain interfaces.

Each pinion gear 118 is integrated with a larger door gear 126.Accordingly, the pinion gears 118 and door gears 126 spin at the sameRPM. The door gears 126 interfaces with door racks 128 of the door 14.Hence, when the door gears 126 turn, the door racks 128 and door 14 moveup or down according to the direction the door gears 126 are spinning.

FIGS. 4B-4E graphically depict a method of loading an assay cartridge.At FIG. 4B, a command is sent to the BLDC motor 100 to open the door 14to place the system into position to accept insertion of the cartridge32. When the command is received, the system 1400 operates the BLDCmotor 100 to turn the lead screw 109. This action causes the bridge 108and affixed rack portions 110/112 to move upwardly, and hence initiateturning of the pinion gears 118 and door gears 126. This movement willcause the door 14 to travel upward as the door gears 126 spin againstthe door racks 128.

After the door 14 is completely open, the pinion gears 118 disengagefrom the racks 114 of the first and second rack portions 110/112, whichcontinue to move upwards. Upward movement of the first and second rackportions 110/112 also causes cartridge loading arms 130 to be actuatedby the pins 132 that are constrained to move along the cam pathways 116of the first and second rack portions 110/112. The cartridge loadingarms 130 are forced by this movement to spin about pivots 134, whichplaces first arm portions 136 into an upward position.

The first and second rack portions 110/112 will move upwardly, until aforce based event occurs that back drives the lead screw 109. Such anevent can be, for example, the bridge 108 encountering a stop or thefirst and second rack portions 110/112 pulling against the cartridgeloading arms 130. The back driving event can be detected at a bridgecircuit of the BLDC motor as a change in current. Based on the backdriving event, the BLDC motor is commanded to stop turning and rest inthe position shown. Advantageously, this step is performed without theaid of any position sensors.

At FIG. 4C, the assay cartridge 32 is inserted into the system 10 untila portion of the assay cartridge 32 is brought into contact with thefirst arm portions 136. Slight movement against the first arm portions136 results in another back driving event at the lead screw 109 that isdetectable at the bridge circuit of the BLDC motor as a change incurrent. This event serves as a command for the BLDC motor to reversedirection from the previous door-opening step in order to capture thecartridge and close the door.

As shown at FIG. 4D, upward movement of the first and second rackportions 110/112 causes the pins 132 to be guided about the length ofthe cam pathways, which in turn causes the cartridge loading arms 130 torotate in a clockwise direction. This causes second arm portions 138 ofthe cartridge loading arms 130 to push the cartridge inward into a homeposition. In addition, the first and second rack portions 110/112 areraised until the fingers 124 of the pinion gears 118 are turned bynotches 140 of the first and second rack portions 110/112, whichinitiates movement of the pinion gears 118 against the rack 114, as wellas the door gears 120 against the door rack 128. In this manner, thedoor 14 is made to travel downward towards a closed position.

As shown at FIG. 4E, the door 14 is made to travel downward by continuedmovement of the lead screw 109 to completely close the door. The BLDCmotor is powered to do so until a force based event occurs that backdrives against the lead screw 109. Such an event can be, for example,the bridge 108 encountering a stop or the first and second rack portions110/112 pushing against the cartridge loading arms 130. The back drivingevent can be detected at the bridge circuit of the BLDC motor as achange in current. Based on detection of the back driving event, theBLDC motor is commanded to stop turning and rest in the position shown.Advantageously, this step is performed without the aid of any positionsensors.

V. Syringe Drive Sub-System

As described above, embodiments of the invention can include aspects ofthe syringe drive mechanism 16. As shown at FIG. 5A, the syringe drivemechanism 16 includes a BLDC motor 200 as described above. The BLDCmotor 200 includes an output shaft that is connected to a back drivablelead screw 209.

A laterally extending arm 206 includes a nut that is threaded to thelead screw 209. The laterally extending arm 206 also is affixed to aplunger rod 208. The laterally extending arm 206 and plunger rod 208 canbe driven downward and upward by commanding the BLDC motor 200 to turnthe lead screw 209 in an appropriate direction.

After the assay cartridge 32 is secured and the door 14 is closed, thesyringe drive mechanism 16 can be utilized to interface with the assaycartridge 32. The assay cartridge includes a syringe passage 210 holdinga plunger tip 212. Downward movement of the plunger rod 208 into thesyringe passage 210, which causes the tip of the plunger rod 208 toengage the plunger tip 212. In this manner, the combined plunger tip 212and plunger rod 208, together with the syringe passage, functions as asyringe to pressurize/depressurize the assay cartridge 32. Programmedpumping of the assay cartridge 32 causes fluid to flow into and out fromvarious chambers of the assay cartridge 32 to affect an assay.

After engagement with the plunger tip 212, the plunger rod 208 can beactuated by the BLDC motor 200 to any desired position within thesyringe passage 210, including enactment of various syringe pumpingalgorithms. Currents of the BLDC motor 200 can be continually monitoredto deliver a consistent pressure to the plunger rod, thus, alleviatingthe need for an in-line pressure sensor to monitor cartridge pressure.

Accordingly, because the lead screw 209 can be back driven, a pressuredecrease within the assay cartridge 32 can cause a stationary plungerrod 208 to be pulled downward. The pressure decrease can be detected bymonitoring the measured current of the BLDC motor 200, detecting arelative change, and then changing the output of the BLDC motor 200accordingly. Similarly, a pressure decrease within the assay cartridge32 can cause a stationary plunger rod 210 to be pushed upward. Thepressure increase can be detected by monitoring the measured current ofthe BLDC motor 200, detecting a relative change, and then changing theoutput of the BLDC motor 200 accordingly. Advantageously, this can beperformed without the aid of any pressure sensors.

In another example, the current associated with a moving plunger rod 208can be monitored for changes that indicate increases or decreases inpressure rate. Hence, after detecting a relative change, the output ofthe BLDC motor 200 can be changed to increase or decrease the pressurerate being applied by the moving plunger rod 208. Advantageously, thiscan be performed without the aid of any pressure sensors.

An example of a method 220, using the aforementioned principles of BLDCcurrent monitoring, for determining proper loading of an assay cartridgeand testing integrity of that cartridge is depicted at FIG. 5B. It isassumed that the assay cartridge 32 has been already physically loadedas shown at FIG. 5A.

At operation 222, a command is sent to begin the loading procedure. As aresult, an over force limit is set at operation 224. The over forcelimit is the maximum force the BLDC motor 200 may exert onto the plungerrod 208 for the purposes of this operation, which is associated with theplunger rod 208 compressing the plunger tip 212 against the bottom ofthe syringe passage 210. At operation 226, the BLDC motor 200 isoperated to move the plunger rod 208 into the syringe passage 210, whichcauses the tip of the plunger rod 208 to engage the plunger tip 212. Atoperation 228 torque of the BLDC motor 200 is continually monitored,using the torque estimation circuit of FIG. 2E and the methodology ofFIGS. 3A-3C, to determine if the plunger rod 208 has travelled to thebottom of the syringe passage 210. If the over force limit is notexceeded then it is determined that the loading procedure has failed atoperation 230. Occasionally, the plunger tip 212 may be missing due to amanufacturing error or physically deficient. In either case, the plungerrod 208 will meet the end of its possible travel with the syringepassage 210 without properly bottoming against a plunger tip 212, andhence, the over force limit will not be exceeded.

If the over force limit is exceeded then it is determined that theplunger rod 208 has pushed the plunger tip 212 to the bottom of thesyringe passage 210, and the method 220 moves to operation 232, where anunder force limit is set. The under force limit is the maximum force theBLDC motor 200 may exert onto the plunger rod 210 for the purposes ofthis operation, which is related to decompressing the plunger tip 212.At operation 234 the BLDC motor 200 is operated to move the plunger rod210 upward within the syringe passage 210. At operation 236 torque ofthe BLDC motor 200 is continually monitored to determine if the underlimit has been exceeded. As a result of operation 228, the plunger tip212 will be highly compressed. The under limit is the amount of forcerequired to decompress the plunger tip and thereby zero out the positionof the plunger tip 212 for later operation. Once the under limit isexceeded, the BLDC motor 200 will cease operation and the method willmove to operation 238, where it is determined if the syringe has drawn avacuum. At this operation, valving of the assay cartridge 32 is operatedto seal off the syringe passage 210 to atmosphere, which was not thecase in the preceding steps. After this is complete, the BLDC motor 200is operated to pull the plunger rod 208 upwards against the vacuumwithin the syringe passage 210. If the plunger rod 208 does not movefreely and force is detected, then at operation 240 it is determinedthat vacuum has been established and thus integrity of the assaycartridge 32 is not comprised. If the plunger rod 208 moves freelywithout detection of force, then at operation 242 it is determined thatno vacuum has been established and thus integrity of the assay cartridge32 is compromised.

Another example of a method 248, using the aforementioned principles ofBLDC current monitoring, for determining initializing the syringe of theassay cartridge (i.e., plunger rod 208, syringe passage 210, and plungertip 212) is depicted at FIG. 5C. It is assumed that the assay cartridge32 has been already physically loaded as shown at FIG. 5A, and thecartridge has been loaded properly as shown at FIG. 5B.

At operation 250, a command is sent to begin the loading procedure. As aresult, an upper force limit is set at operation 252. The over forcelimit is the maximum force the BLDC motor 200 may exert onto the plungerrod 208 for the purposes of this operation, which is associated withplacing the plunger tip 212 at a proper upward position (relative to theorientation of the device as shown in FIG. 5A) at the top of the syringepassage 210.

At operation 254, the BLDC motor 200 is operated to move the plunger rod208 upwardly within the syringe passage 210, which causes the plungertip 212 to top out at a position within the syringe passage 210. Atoperation 256 torque of the BLDC motor 200 is continually monitored,using the torque estimation circuit of FIG. 2E and the methodology ofFIGS. 3A-3C.

Once the over force limit is exceeded then it is determined that theplunger tip 212 is topped out, and the method 248 moves to operation258, where a lower force limit is set. The lower force limit is themaximum force the BLDC motor 200 may exert onto the plunger rod 210 forthe purposes of this operation, which is related to placing the plungertip 212 against the bottom of the syringe passage 210, but withoutexcessive compression of the plunger tip 212. At operation 260 the BLDCmotor 200 is operated to move the plunger rod 210 downwardly within thesyringe passage 210. At operation 262, torque of the BLDC motor 200 iscontinually monitored to determine if the lower force limit set atoperation 258 has been exceeded. Once the lower limit is exceeded, theBLDC motor 200 will cease operation, and it is assumed the plunger tip212 has been placed at the bottom of the syringe passage 210. Afterthis, the method 248 will move to operation 238, where it is determinedif the syringe has moved a predetermined amount of distance (e.g. 60mm). This is performed by using the Hall-effect sensors of the BLDCmotor 200 to count revolutions of lead screw 209 and relating that countto an amount of linear travel of the syringe rod 208. In some cases theupper and lower force limits will be triggered by obstructions orexcessive friction within the syringe passage 210. Hence, the travelcheck step is performed to make sure the syringe rod 208 has movedfreely without obstruction. If the syringe rod 208 has moved at leastthe predetermined amount of travel, then it is determined thatinitialization is successful at operation 266. However, if the syringerod 208 has not moved at least the predetermined amount of travel, thenit is determined that initialization is not successful at operation 268.

VI. Valve Drive Sub-System

As described above, embodiments of the invention can include aspects ofthe valve drive mechanism 20. As shown at FIGS. 6A and 6B, the valvedrive mechanism 20 includes a BLDC motor 300 as described above.

The BLDC motor 300 is mounted to a chassis 304 having a plurality ofreinforcing ribs 306 that contribute to the rigidity of the chassis 304.The chassis 304 includes an elongated first portion 307 that serves as amount for a stator 308 of the BLDC motor 300. An elongated shaft 310extends from the BLDC motor 300 and holds a first worm 312. The firstworm 312 cooperates with and turns a first worm gear 314, which turns ona shaft 316 shared with a second worm 318.

The second worm 318 cooperates with and turns a second worm gear 320.The second worm gear 320 is integrated with a turntable like valve drive322, which is configured to cooperate with a turning valve mechanism ofthe assay cartridge 32. The valve drive 322 is mounted to an elongatedsecond portion 324 of the chassis 304. The elongated second portion 324includes a passage 325 for cooperation with the sonication hornmechanism 22.

In use, the BLDC motor 300 is powered to turn and thereby turns valvedrive 322 via the worm drives described above. The valve drive 322 issubstantially geared down, which allows for great precision whenpositioning the valve drive 322. The syringe drive mechanism 16 does notinclude any position sensors, because angular position of the stator 308can be solely derived from the sinusoidal wave output of the hall-effectsensors, and through that position of the valve drive by knowledge ofthe final drive gear ratio.

The worm drives are not back drivable as in the aforementioned syringedrive and door drive mechanisms. However, the same type of hall-effectposition derivation and force base triggering can be used for the valvedrive mechanism. Here, force base triggering can be indicative of acartridge integrity malfunction. For example, if turning the valve driveunexpectedly requires substantially less or more power, then such anevent can be indicative of a jam or failure of an assay cartridge. Whileeach of the syringe drive, door drive mechanisms and valve drivemechanisms are described as utilizing the improved BLDC motor describedherein, it is appreciated that any or all of the drives and mechanismscould also utilize a conventional type BLDC motor, a servo motor orother suitable motor, as would be understood by one of skill in the art,however some features may require additional sensors or circuitry.

In addition, the BLDC motor is configured to home and center position ofthe valve drive output by performing a centering protocol based on thesinusoidal signal generated by the hall-effect sensors. This cancompensate for gear backlash and gear wear over time. This isillustrated by the Hall voltage signal to valve drive position graphshown at FIG. 6C. As shown, a given position of the valve drive 322 canvary according to gear backlash and wear.

VII. Horn Subassembly

In some embodiments, an ultrasonic horn subassembly is provided for usein an diagnostic assay system as described herein. In some embodiments,the ultrasonic horn assembly includes an ultrasonic horn, a hornhousing, a spring, a chassis and control circuitry configured foroperation of the horn. The horn housing is adapted for supporting andsecuring the ultrasonic horn and includes a section for retaining aspring coil to faciliate movement between a disengaged and engaged hornposition and a wedge for interfacing with a cam mechanism of the systemto actuate movement of the horn between the disengaged (lowered) andengaged (raised) positions. Although a coil spring is described herein,it is appreciated that various other types of springs or biasingmechanisms can be used. In the disengaged position, the tip of theultrasonic horn is flush or below a base surface upon which the assaycartridge sits to facilitate loading and removal of the assay cartridgefrom the system. In the engaged position, the tip of the ultrasonic hornextends above the base surface so as to engage a domed portion of asonication chamber of the assay cartridge to faciltiate sonication ofbiological material in a fluid sample contained within the sonicationchamber during sample analysis preparation and/or processing. In someembodiments, the movement of the horn is effected by an actuatormechanism common to one or more other movable components of the system,such as a door of the system. The horn assembly also includes circuitry,such as a printed circuit board, with interfaces adapted for electricalconnection to corresponding circuitry within the system to faciliateoperation of the ultrasonic horn by the system.

In some embodiments, the diagnostic assay system is placed uprightduring performance of an assay (as shown in FIGS. 9A-B) such that thehorn moves between the disengaged position (lowered below the cartridge)and the engaged position (raised toward the cartridge) so as to engageand contact the sonication chamber of the cartridge. It is appreciatedthat in some embodiments, the design could be different such that in thedisengaged positions and engaged positions the horn could be in variousother orientations and/or locations relative the cartridge depending onthe design of the cartridge and the diagnostic assay system.

VII. A. Horn Subassembly Design and Assembly

FIG. 7A illustrates an ultrasonic horn subassembly 700 configured foruse in a diagnostic assay system in accordance with some embodiments ofthe invention. FIG. 7B depicts an exploded view of the horn assembly ofFIG. 7A. In this embodiment, the horn subassembly includes an ultrasonichorn 710, horn housing 720, spring coil 730, control circuitry 740, andchassis 750. The horn subassembly can be tested as a stand-alonesub-assembly before insertion into the system and may also be removed orreplaced as needed.

FIGS. 8A-E illustrate the components of the horn assembly during variousstages of assembly. As shown in FIG. 8A, ultrasonic horn 710 snaps intothe horn housing 720 (shown cut-away to show the horn residing within).The housing can be designed such that snapping the horn into the housinglocates or clocks the horn within a pre-determined orientation andposition relative the housing. For example, the ultrasonic horn can beof a design that includes features that are not perfectly axi-symmetricabout a longitudinal axis of the horn such that corresponding featuresor surfaces on an interior portion of the housing engage to secure thehorn into position within the housing and inhibit rotation of the horntherein. The non-axi-symmetric feature may include, but is not limitedto, a flat portion on one or both sides of the horn or a protrusion ortab extending outwardly from the horn or a contact through which thehorn is electrically connected.

In some embodiments, the horn 720 is incorporated into the subassemblyand controlled with the control circuitry to provide an output suitablefor lysing biological materials as needed for a particular assay.

As can be seen in FIG. 8A, the outside surface of the horn housing 720includes a spring retention portion 722 for retaining a spring coil 730to effect movement of housing 720 between the disengaged and the engagedpositions. The retaining portion includes an upper retaining surface 722a and a lower retaining surface 722 b that engage the spring when in anon-compressed state. The housing 720 may also include one or more leadretention details 723 to secure and/or guide the leads electricallyconnected to the horn 710 during movement of the horn between thedisengaged/engaged positions. The horn housing 720 includes a wedgeportion 721 for interfacing with a cam of the system.

As shown in FIG. 8C, the partially assembled horn assembly can besnapped into a horn chassis 750. The chassis includes a localizationfeature 751 that engages a corresponding feature of the housing 720 soas to secure the position and orientation of the housing when snapped inplace. The chassis also includes one or more features for securing theentire horn assembly 700 within the diagnostic assay system, forexample, the chassis may include a base portion with one or more holesthrough which the chassis can be mounted to the module. In someembodiments, the chassis is formed of a polymer material by injectionmolding, although it is appreciated that it may be formed of variousother materials (e.g. polymer, ceramic, metal) by various othermanufacturing processes (e.g. pressing, machining, etc.). Afterplacement of the horn assembly into the chassis, a circuitry component740 is attached to the chassis. The chassis may include one or moremounting features 752 a through which the circuitry component (e.g. PCB)can be secured by one or more fasteners or screws 752 b. The circuitrycomponent can be electrically connected to the horn before or after itsattachment to the chassis. The completed horn assembly 700 can then betested and supplied to a user separately or within a diagnostic assaysystem.

VII. B. Sonication Horn Positioning Interface

In some aspects, the ultrasonic horn is mounted on a movable mechanismby which the ultrasonic horn is positioned relative to a sonicationchamber of an assay cartridge disposed within a diagnostic assay system.In some embodiments, the assay cartridge includes a sonication chamberpositioned on the bottom of the cartridge (as oriented in FIG. 10A) witha downward facing dome (outer surface of the dome being convex shapedwith respect to the assay cartridge), as shown in the example of FIG.10A, that corresponds to a rounded tip 711A of the domed output portion711 of the ultrasonic horn. Although the tip is rounded in thisembodiment, it is appreciated that the tip of the dome portion may beshaped in a variety of shapes, including but not limited to flat,pointed, concave, convex, rounded, or domed, as desired. The dome shapedportion of the sonication chamber and the rounded horn tip focus theultrasonic energy transmitted from the horn so as to efficiently reachthe desired ultrasonic levels required to lyse cellular material (e.g.ruggedized cell, spores, etc.) and release DNA into the fluid samplewith minimal ultrasonic horn power and size requirements. It ispreferable for the rounded tip 711 a of the domed output portion 711 ofthe ultrasonic horn to press against the dome 1211 of the sonicationchamber 1210 with sufficient force to ensure contact is maintainedbetween the tip of the horn and the domed shaped surface of thesonication chamber during delivery of ultrasonic energy. In someembodiments, the movable mechanism is configured to move the ultrasonichorn upwards (in the engaging direction) to pressingly engage the domesof the sonication chamber and the ultrasonic horn together with at least0.5 lb-F. In some embodiments, the force applied to ensure that therounded tip of the horn and the dome portion of the sonication chamberis between about 1 lb-F to about 2 lb-F. In some embodiments, the forceapplied is about 1.4 lb-F. Although an interfacing cam and wedge aredescribed herein, it is appreciated that various other mechanisms may beused with or without a biasing member to facilitate movement of the hornbetween the disengaged and engaged positions. For example, in someembodiments, such mechanisms can include a lead screw, cable, and thelike.

In some embodiments, the movable mechanism by which the ultrasonic hornis positioned to press against the sonication chamber is integratedwithin an inter-connector network of actuators that effect movement ofvarious other components of the diagnostic assay system, such as openingand closing of a door of the system, loading and ejection of the assaycartridge from the system, movement of a valve assembly and a syringeassembly within the system. It is appreciated that the movable mechanismmay be integrated with actuators of one or more other components or themovable mechanism may be entirely independent of other mechanisms andactuators.

FIGS. 9A-9B illustrates cross-sectional views of a diagnostic assaysystem during and after loading of an assay cartridge into the systemdemonstrating a mechanism that positions the ultrasonic horn incoordination with closing of a door of the system and loading of theassay cartridge. FIG. 9A depicts a partially inserted assay cartridge 32in which a distal facing portion of a base of the assay cartridge beginsto engage an ejection tooth of an ejection/loading cam 1120. In thisposition of the cam 1120, the outer surface of the cam engages an uppersurface 721 of the wedge portion 721 of the horn housing, as can be seenin more detail in the side-view and cross-section of FIGS. 11A-1 and11A-2 .

As the assay cartridge 32 is more fully inserted, the assay cartridgepresses against the ejection tooth and the ejection/loading cam 1120rotates clock-wise so that a loading tooth of the cam engages anunderside surface of the assay cartridge pulling the cartridge inward toa fully loaded position. As the ejection/loading cam 120 rotates theouter surface 1121 of the cam slides along the wedge tip 721 a of thewedge portion 721 of the horn housing slide, which presses the hornhousing away from the cartridge to the disengage position, which partlycompresses the spring coil 730. As the assay cartridge is fullyinserted, the wedge tip 721 a is received within an inwardly curvedportion 1121 a of the rounded portion of the cam 1120 that allows thehorn housing 720 to move upward a short distance allows the coil to atleast partly uncompress such that the rounded tip 711 a of theultrasonic horn protrudes above the surface along which the assaycartridge was loaded and pressingly engages the dome-shaped portion ofthe sonication chamber. This position can be seen in more detail in theside view and cross-section of FIG. 11B-1 and FIG. 11B-2 , respectively.As can be seen in FIGS. 9A and 9B, rotation of the cam 120 is actuatedby a closing movement of the first rack portion 110 of the door rackmechanism, which in this embodiment is downward movement (in thedirection of the arrow). Through a network of interrelated gears, thisclosing movement of the door also simultaneously actuates closing of thedoor 14 of the system from an open position in FIG. 9A to facilitateinsertion and loading of the assay cartridge 32 to a closed position, asshown in FIG. 9B, after loading of the cartridge. Movement of the doorrack mechanism can be effected by one or more motors, such as any ofthose described herein.

FIG. 10A illustrates a cross-sectional view of an assay cartridge foruse in a diagnostic assay system in accordance with some embodiments ofthe invention. The dome-shaped portion 1211 of the sonication chamber1210, described above, is positioned on the bottom surface of the assaycartridge. The sonication chamber 1210 is in fluid communication with anetwork of channels in the assay cartridge, through which fluid istransported by movement of a valve and syringe to effectuate pressurechanges during the assay procedure. After the sample is prepared and/orprocessed, the prepared fluid sample is transported into a chamber ofthe reaction vessel 33, while an excitation means and an opticaldetection means are used to optically sense the presence or absence of atarget analyte (e.g. a nucleic acid) of interest (e.g., a bacteria, avirus, a pathogen, a toxin, or other target analyte). It is appreciatedthat such a reaction vessel could include various differing chambers,conduits, micro-well arrays for use in detecting the target analyte. Anexemplary use of such a reaction vessel for analyzing a fluid sample isdescribed in commonly assigned U.S. Pat. No. 6,818,185, entitled“Cartridge for Conducting a Chemical Reaction,” filed May 30, 2000, theentire contents of which are incorporate herein by reference for allpurposes.

VII. C. Sonication Horn Control

In some embodiments, operation of the ultrasonic horn is performed byuse of a horn control circuit configured to control current amplitudeand phase estimation in a manner to optimize excitation and provideconsistent robust delivery of ultrasonic power, which is proportional tocurrent at fixed voltage, as needed for a particular assay. In someembodiments, the system provides entirely digital control of sonicationpower delivery. In some embodiments, the system provides operation ofthe ultrasonic horn without conventional transformer and full-waverectification analog circuitry, thereby allowing for decreased powerusage, reduced horn assembly size and an overall reduction in size ofthe system. In some embodiments, the power delivery and control isperformed so as to control real power (which is total power) into theultrasonic horn (as opposed to reactive power). The control circuit isconfigured to apply a programmable sonication power for a programmableduration to the assay cartridge to lyse the target cells as needed for aparticular assay.

In some embodiments, (e.g. with reference to FIG. 12A), an ultrasonichorn includes a mass 713 (typically a solid core of metal) adjacent oneor more piezo-electric actuators 714 that vibrates when connected to apower supply 716 through electrical contacts 715. The solid massincludes a tapered portion 712′ leading to an elongated portion 712 thatfocuses the ultrasonic wave and terminates in a domed output portion 711that further focuses the ultrasonic waves for output at the tip 711 a ofthe domed outputportion 711. Typically, multiple piezo-electricactuators can be used to provide greater ultrasonic output with lowerrelative requirement (as compared to one actuator suited to deliverhigher ultrasonic energies).

In some embodiments, the horn assembly can utilize an off-the-shelf hornwith a horn control circuit that operates the horn with a closed loop orfeedback control that provides consistent, robust ultrasonic energy atdesired levels with lower relative power requirements than wouldotherwise be possible with the horn. For example, such an off-the-shelfhorn having multiple piezo-electric actuators when operated to deliverultrasonic energy levels suitable for lysing of cells in a diagnosticassay may not operate consistently by merely applying a set currentlevel due to the actuators operating out of phase. The piezo-electricactuators expand outward when current is applied and if this outwardexpansion occurs at even slightly different times (out-of-phase), thenthe result is low-frequency coupling into vibration that prevents thehorn from delivering suitable levels of ultrasonic energy. For thisreason, such horns may only operate properly at lower ultrasonic levelsor may not be depended upon to provide consistent delivery of energy forthe duration needed in a particular diagnostic assay.

In some embodiments, the system applies an improved control scheme thatallows for consistent delivery of levels of ultrasonic energy suitablefor lysing of cells in a diagnostic assay for a specified duration usingsuch a horn as described above. In some embodiments, the horn assemblyis configured to employ resonant piezo-electric actuators to applyvibration at a frequency of about 50.5 kHz. In some embodiments the hornassembly is configured to apply vibration frequency in a range fromabout 20 kHz to about 50 kHz. For example, the vibration frequency canbe about 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or about 50 kHz.In some embodiments, the vibration frequency is more than 50 kHz. Insome embodiments, the system utilizes a closed-loop control system toprovide excitation of the piezo-electric that is maintained in-phasewith each other for the duration required for sonication of biologicalmaterial.

In some embodiments, the system applies current and/or voltage to thepiezo-electric actuators by ramping up the applied power to the desiredlevels to minimize occurrences of out-of-phase excitation. An example ofthis scheme is shown in FIG. 10B. In some embodiments, the powerdelivery and control is performed so as to control real power (which istotal power) into the ultrasonic horn (as opposed to reactive power). Bysubstantially maintaining a specified phase relationship between voltageand current, allows reactive power to be substantially eliminated. Thereactive power is when the piezo actuators are not in locked phase andthe horn merely vibrates. By ramping up the power, as opposed to justturning the power on, the ramp allows the system to maintain the phaserelationship between current and voltage and prevent vibration to allowthe horn to deliver the desired ultrasonic energy levels required.

FIG. 12B illustrates a simulated horn power transfer functiondemonstrating the phase relationship between excitation current andvoltage at the power resonance.

In some embodiments, the horn control circuit uses closed control loopsto operate the horn. In an inner control loop, the frequency is adjustedto maintain the present phase relationship. In an outer loop, theamplitude of the voltage excitation is continually adjusted to maintainthe commanded power level. An example of these inner and out controlloops is illustrated in FIG. 14 .

FIG. 13 illustrates a control schematic of the sonication horn assemblyin accordance with some embodiments of the invention. The sonicationinterface is configured in power (Watts) and duration (seconds) asneeded for a particular assay. Typical power levels of 5-10 Watts areapplied for between 15-30 seconds to sufficiently lyse typical sporecells and releasing˜50% of spore-bound DNA into solution within thesample chamber 1210, as shown in FIG. 10B. It is appreciated however,that power, duration and required sonication efficiency vary by assayand can be greater or lesser than the levels described depending onassay needs, design and the type of cells or material being sonicated.In some embodiments, the PSoC DAC generates a 0-4V sine wave. The DACoutput goes through a TI audio amplifier. The TI amplifier multipliesthe signal by 20 db. The TI amplified signal goes through a step uptransformer before being delivered to the horn. Power is estimated bythe voltage (DAC voltage amplified through TI and the transformer) andthe current read by the sensor (P=v*I cos(Φ)) (real power). Thus, powerdelivered to the horn is controlled via controlling the DAC voltage. Acontrol loop drives the input voltage to keep the power at the desiredlevel. See for example FIG. 15 .

In some embodiments, the horn control circuit is configured so that afrequency that gives the highest real power amplitude from a frequencysweep is established as the resonance frequency. The phase between theinput voltage and the output voltage is measured at the resonancefrequency. During sonication, a control loop locks the measured phasebetween input and output voltages by adjusting the input frequency.Current amplitude is a product of sensor factor and the PSoC amplifierthat amplifies the signal before reading. An exemplary relationshipbetween power vs input voltage can be seen in FIG. 16 . An exemplaryrelationship between the horn current amplitude and phase versusfrequency can be seen in FIG. 17 .

In some embodiments, the horn control circuit utilizes a sinusoidalcontrol that controls amplitude input to the horn driver. The circuitcan utilize phase-matching for resonant frequency control to ensure thevoltage and current maintain a specified phase relationship, which canbe used for instance to eliminate reactive power. In some embodiments,the circuit utilizes frequency sweeping with a 1 Hz resolution, however,it is appreciated that this configuration can provide effectivelyunlimited frequency resolution. Such configuration allows for consistentand robust delivery of ultrasonic energy levels with an ultrasonic hornhaving reduced power and size requirements than would otherwise bepossible with such a device.

VIII. Thermal Optical Subassembly

In some embodiments, the invention provides a Thermal OpticalSubassembly (TOS) for use in a diagnostic assay system. In someembodiments, the TOS includes a thermal control device component and anoptical excite/detect component. The TOS may interface with othercomponents of the diagnostic assay system, including the ultrasonichorn, the door, syringe and valve. In some embodiments, the TOS includesa thermal control device instrument and an optical component instrumenthaving an excitation means and an optical detection means. The TOS unitis constructed so as to define a cavity in which a reaction vessel canbe inserted for performing nucleic acid amplification and/or detectionof a target analyte using the thermal control component and opticalinterrogation of the target analyte using the optical componentinstrument. The TOS is employed in a system with one or more circuitboards (e.g. motherboard) that control operation and coordinationbetween the various components of the assay system. In some embodiments,a Cell Core piggy backs onto the motherboard. In some embodiments, eachhardware subassembly carries their own dedicated PSoC processor andassociated electronics. In some embodiments, the diagnositc assay systemincludes a communication means (e.g. wireless, NFC, USB) that allowsmodification and/or updating of the control software or controlparameters utilized by the system. The TOS can also include one or moresensors (e.g. NFC reader) to determine a location or presence of anassay cartridge or a position of the valve component so as to coordinateoperation of multiple components of the system. In some embodiments, theTOS comprises a cartridge position sensor (e.g. NFC reader) locatedphysically on the TOS to allow it to be physically in close proximity tothe assay cartridge when inserted into the diagnostic assay system. Insome embodiments, the TOS can be serially connected other electronicsubsystems via USB and/or wireless interfaces like NFC or bluetooth.

VIII. A. TOS Design

It is appreciated that the thermal control device instrument and theoptical detection device can be defined in various configurations, asdesired. In the embodiments described herein, the thermal control andoptical detection device is configured for use with a reaction vesselhaving two opposing major faces and two edges (minor faces). The thermalcontrol device can be configured for one-sided heating of one major faceof the reaction vessel, or two-sided heating of both the major faces. Inthe embodiments described herein, the thermal control device isconfigured to be positioned adjacent a major face of the reaction vesselon one or both sides. Likewise, the optical detection detection devicecan be configured according to various configurations, such as opticaldetection from a major face of the reaction vessel or from one or moreedges (minor face(s)) of the reaction vessel. Typically, the opticaldetection configuration corresponds to a configuration of the thermalcontrol device, for example, the optical detection device is positionedto detect optics through a part of the reaction vessel not covered bythe thermal control device. In some embodiments, where one sided heatingis used, the opposing non-heated major face can be covered with atransparent insulating material so as to control heat transfer whilestill allowing for optical detection through the insulating material. Insome embodiments, the system utilizes a thermal control deviceconfigured for one-sided heating and an optical detection deviceconfigured for excitation/detection from a major face and/or one or moreedges (minor face) of the reaction vessel. In other embodiments, thesystem utilizes a thermal control device configured for two-sidedheating with an optical detection device configured for opticalexcitation/detection from one or more edges of the reaction vessel.Exemplary configurations are provided below.

FIG. 18 shows an exemplary diagnostic assay system 1000 for performingdetection of a target analyte in a fluid sample prepared within adisposable assay cartridge (not shown) when inserted into the system.The diagnostic assay system 1000 includes multiple components andsubassemblies, as described herein, one of which is the TOS subassembly1100. As shown in FIG. 18 , the TOS 1100 subassembly can install fromthe front of the system. The TOS can be inserted into the frame orhousing of the system 1000 with the door 14 open and secured with one ormore screws (not shown) so that the front plate 1110 faces into thereceptacle of the system that receives the assay cartridge. The frontplate 1110 defines a cavity opening or slot 1111 through which a planarreaction vessel of an assay cartridge can be inserted. In someembodiments, the TOS can be tested as a stand-alone sub-assembly beforeinsertion into the diagnostic assay system. In some embodiments, the TOScan be removed or replaced as needed.

In some embodiments, the diagnostic assay system uses a disposable assaycartridge. An exemplary assay cartridge suitable for use with the systemas described herein is described in U.S. Pat. No. 6,818,185, entitled“Cartridge for Conducting a Chemical Reaction,” filed May 30, 2000, theentire contents of which are incorporate herein by reference for allpurposes.

In some embodiments, the TOS slot 1111 and cavity is dimensioned so asto accommodate the reaction vessel (typically within +/−0.020″) and theoptical mount and associated components are adapted to locate theoptical components relative to the reaction vessel to facilitateexcitation and optical detection for the target analyte. In someembodiments, the TOS is spatially configured to locate a thermal controldevice, such as a dual-TEC device, relative to the reaction vessel tocontrol and facilitate thermal cycling of the fluid sample within thereaction vessel of the assay cartridge. In some embodiments, the TOSmoves the thermal control device, for example, retracting the dual-TECbefore insertion of the reaction vessel and then engages and clamps thedual-TEC against the reaction vessel when the reaction vessel is inplace.

FIGS. 19A-B illustrates front and rear views of an exemplary TOSsub-assembly 1100 in accordance with some embodiments of the invention.In FIG. 19A, an exemplary reaction vessel 33 is shown inserted into thecavity opening 1111 of the front plate 1110 and the thermal controlmount/heat sink 820 can be seen, as well as a cooling fan 822 (see FIG.20B). In FIG. 19B, a rigid flex PCB configuration and thermal contactmechanism 840 allowing for lateral movement of the thermal controldevice prior to clamping engagement of the reaction vessel 33 can beseen. The PCBs 830 and 831 through which the thermal control device 800and the optical component 900 are powered and controlled can be coupledthrough a rigid flex connection 832 that allows for lateral movement.Thermal contact mechanism 840 includes a slidable component thattranslates movement between an open configuration (see FIG. 24B) and aclamped configuration (see FIG. 24A) in which a TEC face 810 of thethermal control device is engaged against the side of a reaction vessel33. In some embodiments, thermal contact mechanism 840 includes amovable and/or adjustable bracket 842 that can slide up and down along avertically extending mount 844 to ensure proper alignment with theoptical component 900 and the reaction vessel, and is movable laterallytoward thermal the thermal control device to ensure suitable thermalcontact with the reaction vessel 33 to facilitate efficient thermalcycling. In some embodiments, the thermal contact mechanism 840 includesa bottom support or guide 846 to facilitate insertion of the reactionvessel within the thermal contact mechanism 840. and the In someembodiments, this movement is effected by axial movement of the doordrive rack 110 as shown in FIGS. 26A-B.

FIGS. 20A-B illustrates exploded views of an example TOS in accordancewith some embodiments of the invention. As can be seen, the TOS assemblyincludes an optical mount 930 having windows through which theexcitation component 910 and optical detection component 920 can operatewhen assembled. The optical mount is attached to the front plate 1110through a bracket 1113 and at least partly surrounds the flange 1112around the reaction vessel opening 1111. The thermal control device 800is coupled to the optical mount 930 by two pins 834 that extend throughthe thermal contact mechanism 840 and two holes through the opticalmount 930. The assembly may also include a sensor for detecting aproximity location, or identity of the cartridge within the system. Insome embodiments, the sensor is a near field communication (NFC) sensor1190, although it is appreciated that various other sensors can be used.It is appreciated that, in some embodiments, the NFC can be adapted todetect various differing things, including but not limited to: thelocation/presence of a cartridge, the type of cartridge, the particularassay, the microfluidic procedures that are unique to a particularassay, the presence of a mobile device (e.g. PDA) and various other lotspecific parameters. In some embodiments, the NFC allows for a work flowassociated with a particular system/cartridge, thereby obviating theneed for a separate database in the cloud that the diagnostic assaysystem would otherwise have to access. This feature is particularlyuseful in a resource limited settings where internet may not be readilyavailable.

FIGS. 21A-B illustrates optical components and associated PCB of anexemplary TOS in accordance with some embodiments of the invention. Theoptical components include an excitation component 910, an opticaldetection component 920 and associated PCB components 830, 831 andelectrical circuitry 833. In some embodiments, the PCBs are connectedthrough a rigid flex connection 832 that allows for lateral movement ofthe thermal control device against the reaction vessel. FIGS. 22A-Billustrates thermal control device components and associated PCB with arigid flex connection in an exemplary TOS. FIGS. 23A-B illustrates athermal control device 800 before being attached to the optical mount930 of an exemplary TOS. In some embodiments, the optical mount 930includes an alignment feature 931 to ensure proper alignment between theoptical component 900 and a reaction chamber portion of the reactionvessel 33. The alignment feature can include one or more features thatengage with corresponding features of the reaction vessel, for example,a hole that receives a distally extending pin of the reaction tube, abump or ridge that engages a corresponding recess of the reactionvessel, a pair of magnets, or any suitable features to facilitatealignment between the reaction vessel and the optical component 900.

FIGS. 24A-24B and 25 illustrate a thermal control device componentmovably coupled to an optical mount and a slide base in accordance withsome embodiments of the invention. In some embodiments, the thermalcontrol mechanism 840 pressingly engages against the reaction vessel ofan assay cartridge. In some embodiments, the force applied to engage thethermal control device against the reaction vessel is at least 1 lbs-F.In some embodiments the amount of force used is between 1 and 3 lb-F,typically about 1.3 lbs-F clamping, to ensure the TEC face staysparallel to and in sufficient contact with a major face of the reactionvessel 33. FIG. 26A-B illustrate operation of the door rack 110effecting lateral movement of the thermal control device between theclamped and open positions (see FIG. 24A-B, respectively).

FIG. 28 illustrates a schematic of the optics module and thermal moduleassembly 810 of the TOS in accordance with some embodiments of theinvention. The optics module includes a detect block chip or detectioncomponent 920 and an excite block chip or excitation component 910disposed on a PCB carrier. FIG. 28 illustrates an exemplary TOS for usein a diagnostic assay system as disclosed herein.

VIII. B. Optical Component

FIG. 30A illustrates an exemplary optical component configuration foruse with a diagnostic assay system as disclosed herein and FIG. 30Billustrates a detailed schematic of an exemplary optical componentconfiguration in accordance with some embodiments of the invention. Insome embodiments, the optical excitation and detection means operatethrough a minor face (edge) of a reaction vessel of an assay cartridgewhile the thermal control device engages against one or more opposingmajor faces of the reaction vessel. In some embodiments, the thermalcontrol device component thermally engages a major face of the reactionvessel on one side. In some embodiments, the thermal control devicecomponent thermally engages a major face of the reaction vessel on bothsides. This latter configuration can be particularly useful for heatingand cooling of larger fluid sample volumes. Such configuirations can useceramic plate heaters to heat and passive cooling (e.g. ambient airblown across the ceramic heaters) means to achieve the thermocycling ofthe fluid in the reaction vessel or can include any of the TECconfigurations described herein.

In accordance with some embodiments of the invention, a miniaturized LEDexcite chip that can excite the fluid sample through a minor edge of thereaction vessel, while a miniaturized detect chip collects fluorescencethrough a major face of the reaction vessel 33, as in the configurationshown in FIG. 30B. In addition, the dual TEC design provides controlledheating and cooling through the opposite face, which provides improvedtemperature control as compared to passive cooling as used in somethermocycling devices. In some reaction vessels, such as theconfiguration in FIG. 30A, edge-looking windows are narrow (about 1.0mm×4.5 mm) and the small size makes traditional lensing difficult.Collecting fluorescence from a major face of the reaction vessel, as inFIG. 30B, provides a larger detection window that allows for more signalto be collected while still allowing excitation and detection to beorthogonal to each other. In some embodiments, the optical detectionchip is sized to match the reaction vessel dimensions. FIG. 30Cillustrates detailed view of each of an exemplary excitation block and adetection block in accordance with some embodiments of the invention. Asshown, excitation block 910 includes LED light sources 911 that directlight through filters and lenses 912 and then rod lenses 913 so as toemit the desired wavelengths of light to the desired locations of thereaction vessel 33. The optical detection block 920 includes photodiodedetectors 921 that detect light emitted from the reaction vessel 33, theemitted light passing through rod lenses 923, and filters and lenses 922before being received by the photodiode detectors 921 so as to ensuredetection of particular wavelengths that may indicate a reaction thatcorresponds to presence of the target analyte within reaction vessel 33.

In some embodiments, the optical component 900 includes an opticalexcitation component 910 and an optical detection component 920positioned on an optical mount adapted to receive a planar reactionvessel 33. The optical excitation component 910 is positioned to emitexcitation energy through an edge (minor face) of a planar surface ofthe reaction vessel 33 and the optical detection component 920 ispositioned along a major planar surface of the reaction vessel. In oneaspect, the optical excitation and optical detection components areorthogonal relative each other. In some embodiments, the opticalcomponents are configured to utilize lenses with a high numericalaperture. In some embodiments, the optical components are configured foroperation at low numerical apertures without requiring use of lenses. Insuch embodiments, the light path may travel from the source, through afilter and to the detection component without requiring use of lenses tofocus the light produced by excitation. Such embodiments can beconfigured such that the excitation and detect light paths are spatiallyarranged relative each other to improve detection of light produced byexcitation at low numerical apertures without requiring use of lenses.Such use of spatial discrimination in detecting of excited light allowsfor light detection without lenses, which allows for a system of reducedsize.

In fluorescent detection systems, the excitation light typically exceedsthe amount of the emitted fluorescent light signal. In order toefficiently detect the emitted signal it is important to collect as muchemitted light as possible. Thus, most conventional systems employ a highnumerical aperture in their optical detection systems. A high numericalaperture allows for collection of more light, which in turn provides forgreater resolution, while a low numerical aperture typically results inthe collection of less light resulting in a lower resolution. Mostconventional fluorescent optical detection systems use a configurationinvolving a lens and a band pass filter in the light path between thelight source and the detector. The filter is typically placed betweenthe lens and the detector such that the lens provides for collimatedlight passing through the filter. In the absence of a lens (andcollimated light) the filter becomes much less efficient as light ofhigh incident angles striking the band pass filter merely passes throughunfiltered. The lens obviates this problem as it collimates (reducingthe high incident angle beams) resulting in more efficient filtering ofthe excitation wavelengths.

In some embodiments of the present invention, the optical system doesnot include a lens. In the absence of a lens, a low numerical apertureconfiguration is used with the light path consisting of just the lightsource, a band pass filter and the detector. Using a low numericalaperture with this configuration reduces the high incident light angles(without using a lens) thus improving the efficiency of the filteringwhich in turn results in a strong signal of emitted light with most ofthe excitation wavelengths filtered out.

In some embodiments, the optics module includes UV, blue, green, yellowand red LEDs, relevant optical filters, coupling optical elements andprotective glass. In some embodiments, the optics device is fullyencapsulated in epoxy, which provides protection from shock and protectsagainst dust and moisture incursion. In some embodiments, the opticsexcitation and detection chips are of reduced size, such as less than 10mm in each dimension, typically about 5 mm (l)×4 mm (w)×3 mm (h).

FIG. 31 illustrates detailed views of the excitation block 910 and thedetection block 920 with an indication of the relative area of theadjacent reaction vessel through which light is emitted from the exciteblock and collected by the detect block.

FIG. 32 illustrates fluorescence detection with the excitation anddetection components of the optical component in accordance with someembodiments of the invention. As can be seen, the configuration in FIG.32 matches the arrangement pattern for the excitation and detectionblocks which relates to the use of the low numerical aperture, inaccordance with some embodiments.

VIII. C. Thermal Control Device

VIII. C. 1. Overview

FIG. 27 illustrates a block control diagram of a thermal control device800 in a TOS board in accordance with some embodiments of the invention.In some embodiments, the thermal control device includes dualthermoelectric coolers (TEC) with a thermal capacitor disposed therebetween. In some embodiments, the thermal control device employs closedloop control utilizing two thermistors to control operation of each TECso as to optimize heating and cooling of the active surface engaged withthe reaction vessel or vessel. This configuration provides lower noise,improved temperature stability, high gain and high band-width, ascompared to conventional temperature control device controls. In someembodiments, one thermal control device is used to heat/cool a fluidsample through a major face of a reaction vessel. In some embodiments, afluid sample is heated/cooled through both major faces of a reactionvessel, using a thermal control device with each major face of thereaction vessel.

In any of the embodiments described which include first and secondthermoelectric coolers, the second thermoelectric cooler can be replacedwith a thermal manipulation device. Such thermal manipulation deviceincludes any of a heater (e.g., a thermoresistive heater), a cooler orany means suitable for adjusting a temperature. In some embodiments, thethermal manipulation device is included in a microenvironment common tothe first thermoelectric cooler such that operation of the thermalmanipulation device changes the temperature of the microenvironmentrelative an ambient temperature. In this aspect, the device changes theambient environment to allow the first thermoelectric cooler to cyclebetween a first temperature (e.g. an amplification temperature between60-70° C.) and a second higher temperature (e.g. a denaturationtemperature of about 95° C.), cycling between these temperatures asrapidly as possible. If both the first and second temperatures are abovethe true ambient temperature, it is more efficient for a second heatsource (e.g. thermoelectric cooler or heater) within a microenvironmentto raise the temperature within the microenvironment above the ambienttemperature. Alternatively, if the ambient temperature exceeds thesecond, higher temperature, the thermal manipulation device could coolthe microenvironment to an ideal temperature to allow rapid cyclingbetween the first and second temperatures more effectively.

In some embodiments, the thermal control device includes a firstthermoelectric cooler having an active face and a reference face, athermal manipulation device, and a controller operatively coupled toeach of the first thermoelectric cooler and the thermal manipulationdevice. The controller can be configured to operate the firstthermoelectric cooler in coordination with the thermal manipulationdevice so as to increase efficiency of the first thermoelectric cooleras a temperature of the active face of the first thermoelectric coolerchanges from an initial temperature to a desired target temperature. Thethermal manipulation devices can include a thermo-resistive heatingelement or a second thermoelectric cooler or any suitable means foradjusting temperature.

In some embodiments, the thermal control device further includes one ormore temperature sensors coupled with the controller and disposed alongor near the first thermoelectric cooler, the thermal manipulation deviceand/or a microenvironment common to the first thermoelectric cooler andthe thermal manipulation device. The thermal manipulation device can bethermally coupled with the first thermoelectric cooler through amicroenvironment defined within a diagnostic assay system in which thethermal manipulation device is disposed such that a temperature of themicroenvironment can be controlled and adjusted from an ambienttemperature outside of the system.

In some embodiments, the thermal control device includes a controllercoupled with each of the thermoelectric cooler and the thermalmanipulation device that is configured to control temperature so as tocontrol a temperature within a chamber of a reaction vessel in thermalcommunication with the thermal control device. In some embodiments, thecontroller is configured to operate the first thermoelectric coolerbased on thermal modeling of an in situ reaction chamber temperaturewithin the reaction vessel. The thermal modeling can be performed inreal-time and can utilize Kalman filtering depending on the accuracy ofthe model.

In some embodiments, the thermal control device is disposed within andevice diagnostic assay system and positioned to be in thermalcommunication with a reaction vessel of an assay cartridge disposedwithin the system. The controller can be configured to perform thermalcycling in a polymerase chain reaction process within a chamber of thereaction vessel.

In some embodiments, the thermal control device includes a firstthermoelectric cooler having an active face and a reference face, athermal manipulation device, a thermal interposer disposed between thefirst thermoelectric coolers and the thermal manipulation device suchthat the reference face of the first thermoelectric cooler is thermallycoupled with the thermal manipulation device through the thermalinterposer (which can be a thermal capacitor as disclosed herein), and afirst temperature sensor adapted to sense the temperature of the activeface of the first thermoelectric cooler. The device can further includea controller operatively coupled to each of the first thermoelectriccooler and the thermal manipulation device. The controller can beconfigured to operate the thermal manipulation device in coordinationwith the first thermoelectric cooler to increase speed and efficiency ofthe first thermoelectric cooler as a temperature of the active face ofthe first thermoelectric cooler is changed from an initial temperatureto a desired target temperature. In some embodiments, the controller isconfigured with a closed control loop having a feedback input of apredicted temperature based on a thermal model that includes an inputfrom the first temperature sensor.

Various aspects of such a thermal control device are described in detailin concurrently filed, U.S. Non-Provisional application Ser. No.15/217,902, entitled, “Thermal Control Device and Methods of Use,” filedon Jul. 22, 2016, the entire contents of which are incorporated hereinby reference for all purposes. It is appreciated that a thermal controldevice used in a TOS system in accordance with some embodiments of theinvention can include any combination of elements as described therein.

VIII. C. 2. TEC Design

In some embodiments, the thermal control device includes a first TEChaving an active face and a reference face; a second TEC having anactive face and a reference face; and a thermal interposer disposedbetween the first and second TECs such that the reference face of thefirst TEC is thermally coupled with the active face of the second TECthrough the thermal interposer. In some embodiments, the thermalinterposer acts as a thermal capacitor. In some embodiments, the thermalcontrol device includes a controller operatively coupled to each of thefirst and second TECs, the controller configured to operate the secondTEC concurrent with the first TEC so as to increase the speed andefficiency in operation of the first TEC as a temperature of the activeface of the first TEC changes from an initial temperature to a desiredtarget temperature. In some embodiments, the first and secondthermoelectric coolers are thermally coupled through a thermal capacitorwith sufficient thermal conductivity and mass to transfer and storethermal energy so as to reduce time when switching between heating andcooling, thereby providing faster and more efficient thermal cycling. Insome embodiments, the device utilizes a thermocouple within the firstthermoelectric cooler device and another thermocouple within the thermalcapacitor layer and operates using first and second closed control loopsbased on the temperature of the first and second thermocouple,respectively. In order to utilize the stored thermal energy in thethermal capacitor layer, the second control loop may be configured tolead or lag the first control loop. By using one or more of theseaspects described herein, embodiments of the present invention provide afaster, more robust thermal control device for performing rapid thermalcycling, preferably in about two hours or less, even in problematic hightemperature environments described above.

In some embodiments, the thermal control device includes a thermalcapacitor formed of a thermally conductive material of sufficient massto store thermal energy sufficiently to facilitate increased speed inswitching between thermal cycles and efficiency in heating and coolingof a TEC. In some embodiments, the thermal capacitor includes a materialhaving higher thermal mass than that of the active and reference facesof the first and second TECs, which can be formed of a ceramic material.In some embodiments, the thermal capacitor is formed of a layer ofcopper with a thickness of about 10 mm or less, (e.g., about 10, 9, 8,7, 6, 5, 4, 3, 2, or 1 mm, or less). This configuration allows for athermal control device of a relatively thin, planar construction so asto be suitable for use with a reaction vessel in a nucleic acid analysisdevice of reduced size.

In some embodiments, the thermal control device includes a firsttemperature sensor adapted to sense the temperature of the active faceof the first TEC; and a second temperature sensor adapted to sense atemperature of the thermal capacitor. In some embodiments, the first andsecond temperature sensors are coupled with the controller such thatoperation of the first and second TECs is based, at least in part, on aninput from the first and second temperature sensors to the controller,respectively. In some embodiments, the second temperature sensor isembedded or at least in thermal contact with the thermally conductivematerial of the thermal capacitor. It is appreciated that in any of theembodiments described herein the temperature sensor may be disposed invarious other locations so long as the sensor is in thermal contact withthe respective layer sufficiently to sense temperature of the layer.

In some embodiments, the thermal control device includes a controllerconfigured with a primary control loop into which the input of the firsttemperature sensor is provided, and a secondary control loop into whichthe input of the second temperature sensor is provided. The controllercan be configured such that a bandwidth response of the primary controlloop is timed faster (or slower) than a bandwidth response of thesecondary control loop. Typically, both the primary and secondarycontrol loops are closed-loop. In some embodiments, the controller isconfigured to cycle between a heating cycle in which the active face ofthe first TEC is heated to an elevated target temperature and a coolingcycle in which the active face of the first TEC is cooled to a reducedtarget temperature. The controller can be configured such that thesecondary control loop switches the second TEC between heating andcooling modes before the first control loop is switched between heatingand cooling so as to thermally load the thermal capacitor. In someembodiments, the secondary control loop maintains a temperature of thethermal capacitor within about 40° C. from the temperature of the activeface of the first TEC. In some embodiments, the secondary control loopmaintains a temperature of the thermal capacitor within about 5, 10, 15,20, 25, 30, 35, 40, 45, or 50 degrees C. from the temperature of theactive face of the first TEC. The controller can be configured such thatefficiency of the first TEC is maintained by operation of the second TECsuch that heating and cooling with the active face of the first TECoccurs at a ramp rate of about 10° C. per second. Non-limiting exemplaryramp rates that can be achieved with the instant invention include 20,19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1° C.per second. In some embodiments, the elevated target temperature isabout 90° C. or greater and the reduced target temperature is about 40°C. or less. In some embodiments, the elevated temperature is about 95°C. and the reduced target temperature is in a range from about 60° C. toabout 75° C., including all temperatures in between the ends of therange.

In some embodiments, the thermal control device further includes a heatsink coupled with the reference face of the second TEC to preventthermal runaway during cycling. The thermal control device may beconstructed in a generally planar configuration and dimensioned tocorrespond to a planar reaction chamber portion of a reaction vessel ofan assay cartridge. In some embodiments, the planar size has a length ofabout 45 mm or less and a width of about 20 mm or less, or a length ofabout 40 mm by about 12.5 mm, such as about 11 mm by 13 mm, so as to besuitable for use with a reaction vessel in a miniature PCR analysisdevice. The generally planar configuration can be configured anddimensioned to have a thickness from an active face of the first TEC toan opposite facing side of the heat sink of about 20 mm or less.Advantageously, in some embodiments, the thermal control device can beadapted to engage with a reaction vessel for thermal cycling of thereaction vessel on a single side thereof to allow optical detection of atarget analyte from an opposing side of the reaction vessel duringthermal cycling.

In some embodiments, methods of controlling temperature are providedherein. Such methods include steps of: operating a first TEC having anactive face and a reference face to heat and/or cool the active facefrom an initial temperature to a target temperature; and operating asecond TEC having an active face and a reference face so as to increaseefficiency of the first TEC as the temperature of the active face of thefirst TEC changes from the initial temperature to the desired targettemperature, the active face of the second TEC being thermally coupledto the reference face of the first TEC through a thermal capacitor. Suchmethods can further include steps of: operating the first TEC comprisesoperating a primary control loop having a temperature input from atemperature sensor at the active face of the first TEC, and operatingthe second TEC comprises operating a secondary control loop having atemperature input from a temperature sensor within the thermalcapacitor. In some embodiments, the method further includes: cyclingbetween a heating mode in which the active face of the firstthermoelectric device heats to an elevated target temperature and acooling mode in which the active face is cooled to a reduced targettemperature; and storing thermal energy from thermal fluctuationsbetween the heating and cooling modes in the thermal capacitor, thethermal capacitor comprising a layer having increased thermalconductivity as compared to the active and reference faces of the firstand second thermoelectric cooling devices, respectively.

In some embodiments, methods of controlling temperature in thermalcycling include: cycling between a heating mode and a cooling mode ofthe second thermoelectric device concurrent with cycling between theheating and cooling modes of the first thermoelectric device therebymaintaining efficiency of the first thermoelectric device duringcycling. In some embodiments, the controller is configured such that abandwidth response of the primary control loop is faster than abandwidth response of the secondary control loop. The controller canfurther be configured such that cycling is timed by the controller toswitch the second thermoelectric device between modes before switchingof the first thermoelectric device between modes so as to thermally loadthe thermal capacitor. In some embodiments, the elevated targettemperature is about 95° C. or greater and the reduced targettemperature is about 50° C. or less. In some embodiments, methods ofcontrolling temperature further include: maintaining a temperature ofthe thermal capacitor within about 40° C. from the temperature of theactive face of the first TEC by controlled operation of the second TECduring cycling of the first TEC so as to maintain an efficiency of thefirst TEC during cycling. In some embodiments, the efficiency of thefirst TEC is maintained by operation of the second TEC such that heatingand/or cooling with the active face of the first TEC occurs at a ramprate of within 10° C. per second or less. Such methods may furtherinclude: operating a heat sink coupled with the reference face of thesecond TEC during cycling with the first and second TECs so as toprevent thermal runaway.

In some embodiments, methods of thermal cycling in a polymerase chainreaction process are provided herein. Such methods may include steps of:engaging a thermal control device with a reaction vessel having a fluidsample therein for performing a polymerase chain reaction for amplifyinga target polynucleotide such that the active face of the first TECthermally engages the reaction vessel; and thermal cycling the thermalcontrol device according to a particular protocol for amplifying thetarget polynucleotide contained in the fluid sample. In someembodiments, engaging the thermal control device with the reactionvessel comprises engaging the active face of the first TEC against oneside of the reaction vessel such that an opposite side remains uncoveredby the thermal device to allow optical detection from the opposite side.In some embodiments, each of the heating mode and cooling mode use oneor more operative parameters, wherein the one or more operativeparameters are asymmetric between the heating and cooling mode. Forexample, each of the heating mode and cooling mode has a bandwidth and aloop gain, wherein the band width and the loop gains of the heating modeand cooling mode are different.

In some embodiments, methods of controlling temperature with a thermalcontrol device are provided. Such methods include steps of: providing athermal control device a first and second TEC with a thermal capacitorthere between, wherein each of the first and second TECs have an activeface and a reference face; heating the active face; cooling the activeface; heating the reference face; and cooling the reference face. Insome embodiments, each of heating the active face and cooling the activeface is controlled by one or more operative parameters. In someembodiments, a magnitude of the one or more operative parameters isdifferent during heating the active face as compared to cooling theactive face.

In some embodiments, methods include reliability testing betweenmultiple thermal control devices by use of an alternating fixture. Suchmethods include steps of: alternating thermal cycling among the thermalcontrol device and a second or more thermal control devices, to effectthermal cycling of a second or more reaction vessels by operating afixture that alternatingly positions the thermal control device and thesecond or more thermal control devices at an active location at whichthermal cycling of the respective reaction vessel is performed. In someembodiments, the fixture is a rotatable hub with the thermal controldevice and the two or more thermal control devices distributedcircumferentially about an outside of the hub such that operating thefixture comprises rotating the hub.

VIII. C. 2. a. Example TEC Design Configurations

FIG. 33A shows an exemplary thermal control device that includes a firstTEC 811 (primary TEC) and a second thermal manipulation device, such assecondary TEC 812 or thermo-resistive element) thermally coupled througha thermal capacitor 813, also referred to as a thermal interposer. TheTECs are configured such that an active face 811 a of the first TEC 811is thermally coupled with a reaction vessel 33 to facilitate controllingthermal cycling therein. The device can optionally include a couplingfixture 819 for mounting the device on the tube. In some embodiments,the device can be secured to a fixture that positions the deviceadjacent the tube. The opposing reference face 811 b of the first TEC isthermally coupled with an active face 812 a of the second TEC 812through the thermal capacitor layer. This configuration may also bedescribed as the reference face 811 b being in direct thermal contactwith one side of the thermal capacitor layer 813 and the active face 812a being in direct thermal contact with the opposite side of the thermalcapacitor layer 813. In some embodiments, the reference face 812 b ofthe second TEC is thermally coupled with a heat sink 817 and/or acooling fan 818, such as shown in the embodiment of FIG. 33B. In thisembodiment, the thermal control device 800 is configured such that it isthermally coupled along one side of a planar portion of the reactionvessel 33 so as to allow optical excitation from another direction (e.g.a side of the tube) with an optical excitation means 910, such as alaser, and optical detection from another direction (e.g. an oppositeside of the tube) with an optical detection means 920.

A thermocouple 816 is included in the first TEC 811 at or near theactive face 811 a to allow precise control of the temperature of thereaction vessel. The temperature output of this thermocouple is used ina primary control loop 814 that controls heating and cooling with activeface 11 a. A second thermocouple 816′ is included within or near thethermal capacitor layer and an associated temperature output is used ina second control loop 814′ that control heating and cooling with theactive face 812 a of the second TEC. In one aspect, the first controlloop is faster than the second control loop (e.g. the second controlloop lags the first), which accounts for thermal energy transferred andstored within the thermal capacitor layer. By use of the these twocontrol loops, the temperature differential between the active face 811a and the reference face 811 b of the first TEC 811 can be controlled soas to optimize and improve efficiency of the first TEC, which allows forfaster and more consistent heating and cooling with the first TEC, whilethe thermal capacitor allows for more rapid switching between heatingand cooling, as described herein and demonstrated in the experimentalresults presented below.

Instead of bonding a standard heat-sink to the ceramic plate oppositethe reaction vessel, another (secondary) TEC is used to maintain atemperature within about 40° C. of the active face of the primary TEC.In some embodiments, two PID (Proportional Integral Derivative gain)control loops are used to maintain this operation. In some embodiments,non-PID control loops are used to maintain the temperature of the activeface of the primary TEC. Typically, a fast PID control loop drives theprimary TEC to a predetermined temperature setpoint, monitored by athermistor mounted to the underside of the ceramic plate in contact withthe reaction vessel. This loop operates with maximum speed to ensure thecontrol temperature can be quickly and accurately reached. In someembodiments, a second, slower PID control loop maintains the temperaturefor the bottom face of the primary TEC to maximize thermal efficiency(experimentally determined to be within ˜40° C. from the active facetemperature). As discussed above, non-PID control loops can also be usedto maintain the temperature of the TEC to maximize thermal efficiency.In some embodiments, it is advantageous to dampen the interactionbetween the two control loops to eliminate one loop from controlling theother. It is further advantageous to absorb and store thermal energyfrom the first and/or second TEC by use of the thermal capacitor layerto facilitate rapid switching between heating and cooling.

Two non-limiting exemplary ways to achieve rapid and efficient switchingbetween heating and cooling as used in some embodiments of the inventionare detailed herein. First, the bandwidth response for the secondarycontrol loop is intentionally limited to be much lower than the fastprimary loop, a so-called “lazy loop.” Second, a thermal capacitor issandwiched between two TECs. While it is desirable for the entirethermal control device to be relatively thin to allow use of the deviceon a reaction chamber portion of a reaction vessel, it is appreciatedthat the thermal capacitor layer may be thicker so long as it providessufficient mass and conductivity to function as a thermal capacitor forthe TECs on either side. In some embodiments, the thermal capacitorlayer is a thin copper plate of about 1 mm thickness or less. Copper isadvantageous because of its extremely high thermal conductivity, while 1mm thickness is experimentally determined to sufficiently dampen the twoTECs while providing sufficient mass for the thin layer to store thermalenergy so as to act as a thermal capacitor. While copper is particularlyuseful due to its thermal conductivity and high mass, it is appreciatedthat various other metals or materials having similar thermalconductivity properties and high mass can be used, preferably materialsthat are thermally conductive (even if less than either TEC) and with amass the same or higher than either TEC to allow the layer to operate asa thermal capacitor in storing thermal energy. In another aspect, thethermal capacitor layer may contain a second thermistor which is used tomonitor the “backside” temperature (e.g. reference face) used by thesecondary PID control loop. Both control loops can be digitallyimplemented within a single PSoC (Programmable System on Chip) chipwhich sends control signals to two bipolar Peltier current supplies. Itwill be appreciated by the skilled artisan that in some embodiments,non-PSOC chips can be used for control, e.g., field programmable gatearrays (FPGAs) and the like are suitable for use with the instantinvention. In some embodiments, the dual-TEC module includes a heat-sinkto prevent thermal runaway, which can be bonded to the backside of thesecondary TEC using, e.g., thermally-conductive silver epoxy.Alternative bonding methods and materials suitable for use with theinvention are well known to persons of skill in the art.

FIG. 33B shows a schematic of dual-TEC design. Temperature of the PCRreaction vessel (measured by a thermistor, (16) (ellipse) is governed bythe primary TEC and controlled by a loop in PSoC firmware. Optimalthermal efficiency of the Primary TEC is maintained by a secondthermistor (816′) (ellipse) in thermal contact with a copper layer,which feeds into a secondary PSoC loop, controlling a second TEC.

VIII. C. 2. b. Initial Dual-TEC Fabrication

FIG. 33C shows an example dual-TEC heating/cooling module with a thermalcontrol device 800 thermally engaged against one major face of thereaction vessel, an optical excite block adjacent a minor face (e.g.edge) of the reaction vessel, and an optical detect block 920 against anopposing major face of the reaction vessel 33. In some embodiments, bothPrimary and Secondary TECs (Laird, OptoTEC HOT20,65,F2A,1312, datasheetbelow) measure 13 (w)×13 (I)×2.2 (t) mm, and have a maximum thermalefficiency=60%. In some embodiments, the planar area affected by the TECmodule is matched to the GX reaction vessel. In some embodiments, it isconfigured to accommodate reaction vessels ranging from 25 μl to 100 μl.

FIG. 33B shows an exemplary dual-TEC module for single-sided heating andcooling of a reaction vessel in a chemical analysis system. It isappreciated that this design could be modified to provide the dual-TECon both sides for double-sided heating in some embodiments. As can beseen, the heat-sink includes a mini-fan to flush heat and maintain TECefficiency. The primary TEC (top) cycles temperature in the reactionvessel, monitored by a thermistor mounted to the under-side of theceramic in contact with the tube. The “backside” TEC maintains thetemperature of an interstitial copper layer (by use of a thermistor) toensure optimal thermal efficiency of the primary TEC. A heat-sink withintegrated mini-fan keeps entire module at thermal equilibrium.

In some embodiments, a small thermistor with +/−0.1° C. temperaturetolerance is bonded to the underside of top face of the primary TECusing silver epoxy. This thermistor probes the temperature applied tothe reaction vessel and is an input for the primary control loop in thePSoC, which controls the drive current to the primary TEC. The bottomsurface of the primary TEC is bonded to a 1 mm-thick copper plate withsilver epoxy. The copper plate has a slot containing a second TR136-170thermistor, potted with silver epoxy to monitor “backside temperature,”the signal input for the secondary control loop in the PSoC. Thesecondary TEC, controlled by the secondary control loop, is thensandwiched between the copper plate and an aluminum heat-sink. Theheat-sink is machined to an overall thickness=6.5 mm, keeping the entirepackage <13 mm thick, and a planar size=40.0(l)×12.5(w) mm, necessitatedby space constraints within an instrument of reduced size. A 12×12 mmSunon Mighty Mini Fan (datasheet below) is glued within an insetmachined into the heat-sink where the TECs interact with the heat-sink.Note the mini-fan does not need to directly cool the heat-sink; a quiet,durable, cheap, low-voltage (3.3V max) brushless motor is sufficient tomaintain heat-sink performance by removing hot surface air from thealuminum/air interface using shear flow, as opposed to direct aircooling (as in some conventional analysis devices).

Testing of prototype units can be used to determine whetherheating/cooling speed, thermal stability, robustness with increasedambient temperature, and overall system reliability is sufficient tomeet engineering requirement specifications. Thermal performance hasbeen shown acceptable such that the design goals are met for anexemplary reduced size system: smaller size, robust, and inexpensive(fewer parts needed than with two-sided heating/cooling). Further,single-sided heating/cooling enables more efficient optical detectionthrough the side of the reaction vessel.

FIG. 33C shows a CAD drawing of the dual-TEC heating/cooling module, aswell as the LED Excite- and Detect-Blocks, and the reaction vesselwithin an exemplary system. The reaction vessel is thermal-cycled on oneside (first major face of the reaction vessel) and fluorescence detectedthrough the opposite side (second major face of the reaction vessel).LED illumination remains through the edge (minor face) of the reactionvessel.

VIII. C. 2. c. Initial Heating/Cooling Performance

Heating and cooling performance of the exemplary TEC assembly wasmeasured using a custom fixture that securely clamps the TEC assemblyagainst one surface of a reaction vessel. Care was taken to thermallyisolate the TEC assembly from the fixture by making it of thermallyinsulating Delrin. To mimic a thermal load of a PCR, the reaction vesselwas filled with a fluid sample which was in secure contact with afluorescent detect block on the tube surface opposite the TEC assembly.It should be noted the temperature on the top TEC surface contacting thetube in this geometry was independently measured to be equal or higherthan the temperature measured on the primary TEC thermistor. Therefore,it is reasonable to use the read temperature of the primary TECthermistor to initially characterize thermal performance of the dual-TECheating/cooling system. Any mismatch between thermistor and reactionvessel temperature can be characterized and adjusted for using feedbackloops between the primary TEC thermistor and the temperature of thefluid sample in the reaction vessel.

In some embodiments, a clamping fixture is used to secure the thermalcontrol device to a reaction vessel for thermal characterization. In oneexample, a reaction vessel can be filled with a fluid sample and securedto make thermal contact between the heating/cooling module and one faceof the reaction vessel. The other face of the tube can be clampedagainst a fluorescent detect block. An LED excite block illuminates thesolution through the edge of the tube. In some embodiments bothexcitation and detection are done through minor faces of the tube.

In some embodiments, a PSoC control board employs PID control tomaintain a temperature setpoint of the primary TEC thermistor and toprovide dual-polarity drive current to the TEC devices (positive voltagewhen heating, negative voltage when cooling), and to power the mini-fan.This PID loop was tuned to maximize performance of the primary TEC. Ascript was written to cycle the set-point of the tube between high andlow temperature extremes characteristic of PCR thermo-cycling.Specifically, the low temperature set-point=50° C., with a dwell time 12sec, beginning once the measured temperature is within +/−0.1° C. for a1 sec. Similarly, the high-temperature set-point=95° C. for 12 sec,beginning once the temperature is maintained +/−0.1° C. from thesetpoint for 1 sec. The script cycled between 50° C. and 95° C. adinfinitum.

The secondary control loop was also maintained within the same PSoCchip, reading the temperature of the secondary thermistor in thermalcontact with the copper dampening/thermal capacitor layer (see FIG. 33A)and acting upon the secondary TEC. A different set of PID tuningparameters was found to properly maintain system thermal performance bycontrolling the temperature of this copper layer, so-called the“backside” temperature. This control loop had a significantly lowerbandwidth than the primary TEC control loop, as expected. The PSoC andassociated program also allow multiple set-points of backsidetemperature, which is useful in maximizing ramp rate performance bykeeping the primary TEC operating under optimally efficient thermalconditions.

FIG. 34 shows an exemplary thermal cycle from a reaction vesseltemperature, the traces measured for a thermal cycle from 50° C.→95°C.→50° C. (Primary trace) under closed-loop control. Closed-loop heatingand cooling rates are ˜7° C./sec. The control primary is the desiredtemperature set-point of the thermal cycle (the square function between0 seconds and 20 seconds elapsed time) and the primary trace is themeasured temperature of the tube. As can be seen, the actual thermalcycle lags the desired thermal cycle indicated by the control primaryfunction. It was determined that the thermal efficiency of the primaryTEC was highest with a temperature differential between the tube and thebackside of no higher than 30° C., so the backside temperature wascontrolled to be 65° C. when heating to maximum temperature (tube 95°C.) and 45° C. when cooling the tube to 50° C. (backside trace). Oncethe primary TEC has ramped to higher temperature, the backsidetemperature could be slowly and controllably driven to a lowertemperature in anticipation of the next thermal cycle shown starting atabout 37 seconds elapsed time). This scheme is analogous to using thebackside TEC to properly load a “thermal spring” acting upon the primaryTEC, and is applicable for use with PCR systems, because the thermalprofile to be applied for a particular PCR assay is known a priori by anassay designer. Note the closed-loop ramp rate for stable and repeatableheating and cooling is 6.5 seconds for the 45° C. range, as shown forten successive thermal cycles, as shown in FIG. 35 , corresponding to atrue closed loop ramp rate ˜7° C./sec for both heating and cooling.Performance is maintained throughout multiple cycles over the full PCRthermo-cycling range.

VIII. C. 2. d. Early and Near-Term Reliability Experiments

A typical PCR assay has about 40 thermal cycles from the annealtemperature (˜65° C.) to the DNA denaturation temperature (˜95° C.) andback to the anneal temperature. For assessing reliability, an exemplarythermal control module was cycled between 50° C. (on the order of theminimum temperatures used for PCR experiments) and 95° C., with a 10 secwait time at each temperature to enable system thermal equilibrium.

FIG. 36A shows a comparison of the first and final 5 cycles of a 5,000cycle test. Note the time axis of the trace on the right is from a smalldata-sampling range; 5,000 cycles took approximately 2 days. This modulehas since been cycled over 10,000 times with maintained performance. Ascan be seen, thermo-cycling performance for cycles 1-5 (left) remainsconstant after 5,000 cycles (cycles 4,995-5,000 at right) and there isno change in the thermal performance between the initial and finalcycles. This is encouraging for two reasons. First, closed-loopparameters for rapid heating/cooling are quite stable with repeatedthermal cycling. Even small thermal instability leads to drift inmeasured temperature curves for both the primary and backside TECs,quickly escalating to thermal runaway (which would induce anover-current shutdown fault in the firmware). Properly-tuned systems didnot display this behavior, demonstrating the robustness of the system.Second, the thermal efficiency of the module is stable over 5,000cycles. Indeed, this unit has subsequently been cycled >10,000 timeswithout catastrophic or gradual erosion of performance. FIG. 36B showsthermo-cycling performance for five cycles at the beginning of thermalcycling and after two days of continuous thermal cycling.

VIII. D. Thermal Modeling Approach for Controlling Thermal Cycling

In another aspect, the thermal control device can be configured tocontrol temperature based on thermal modeling. This aspect can be usedin thermal control device configured for one-sided heating or two-sidedheating. In some embodiments, such devices include a firstthermoelectric cooler and another thermal manipulation device, eachbeing coupled to a controller that controls the first thermoelectriccooler in coordination with the thermal manipulation device to improvecontrol, speed and efficiency in heating and/or cooling with the firstthermoelectric cooler. It is appreciated, however, that this thermalmodeling aspect can be incorporated into the controls of any of theconfigurations described herein.

An example of such an approach is illustrated in the state model diagramshown in FIG. 37 . This figure illustrates a seven state model for usewith a single-sided version of the thermal control device. This modelapplies electrical theories to model real world thermal system of thetemperature that include the temperatures of the thermoelectric coolerfaces, the reaction vessel or vessel, and the fluid sample within thereaction vessel. The diagram shows the seven states of the model and thethree measured states used in the Kalman algorithm to arrive at anoptimal estimation of the reaction vessel contents assuming it is water.

In the circuit model of FIG. 37 , capacitors represent material thermalcapacitance, resistors represent material thermal conductivity, voltageat each capacitor and source represents temperature, and the currentsource represents thermal power input from the front side thermoelectriccooler (TEC), adjacent to the tube face. In this embodiment, inputs tothe model are the backside TEC temperature which can be predicted frommodel T1-T7, the front side thermoelectric cooler heat input (Watts),and the “Block” temperature which lies adjacent to the opposite vesselor tube face. This completes the model portion of the algorithm. Aspreviously noted, Kalman algorithms typically use a model in conjunctionwith measured sensor signal/signals that are also part of the modeloutputs. Here, the measured thermistor signals converted to temperatureare used for the front side thermoelectric cooler, and also for thebackside thermoelectric cooler. For the case of the backside measuredtemperature, it is not an output of the model, but it is assumed thatthey are the same. One reason for this assumption is that the R1 isnegligible in terms of overall thermal conductance.

VIII. C. 2. e. Alternative TEC Designs

Variability in module construction can cause slight differences indevice performance. For example, current modules are hand-assembled,with machined heat-sinks and interstitial copper layers, and allcomponents are bonded together by hand using conductive epoxy. Variationin epoxy thickness or creation of small angles between components withinthe module's sandwich construction cause different thermal performance.Most significantly, thermistors are also attached to the ceramic usingthermal epoxy. Small gaps between the thermistor and ceramic lead toerrors between the control and measured temperatures. Finally, it isvery time-consuming to solder the small wires to make electricalcontacts for the two TECs, two thermistors, and the fan power leads.

In some embodiments, the thermal device includes a heating and coolingsurface (e.g. TEC device as described herein) on each major face(opposing sides) of the reaction vessel. In such embodiments, opticaldetection can be performed along the minor face (e.g. edge). In someembodiments, optical detection is performed along a first minor face andoptical excitation is performed along a second minor face that isorthogonal to the first minor face. Such embodiments may be particularlyuseful where heating and cooling of larger volumes are needed (100-500μl fluid samples).

In some embodiments, the thermal control device modules use a customPeltier device that contains an integrated surface-mount thermistormounted onto the underside of the ceramic plate in contact with thereaction vessel. A tiny, 0201 package thermistor (0.60 (l)×0.30 (w)×0.23(t) mm) can be used to minimize convection inside the Peltier deviceleading to temperature variation by limiting the part thickness. Also,because thermal contact and position of surface-mount thermistors can beprecisely controlled, these parts will have very consistent,characterizable differences between the measured and the actual ceramictemperature.

In some embodiments, the thermal control device can include customPeltiers designed to be fully integrated into a heating/cooling moduleusing semi-conductor mass-production techniques (“pick and place”machines and reflow soldering). The interstitial copper substrate can besubstituted for a Bergquist thermal interface PC board (1 mm-thickcopper substrate), which have precisely controlled copper thickness andpad dimensions. The Bergquist substrates will also provide pad leads forthe backside thermistor and all electrical connections into and out ofthe module. The backside Peltier will remain a device similar to what iscurrently used. Finally, the entire TEC assembly can be encapsulated insilicone to make it water resistant. In some embodiments, an aluminummounting bracket can also double as a heat-sink.

IX. Diagnostic Platform

FIG. 38 is a simplified block diagram illustrating an architecturaloverview of a diagnostic assay system, according to some embodiments ofthe invention. As with all FIGS. shown herein, various embodiments maydiffer from the examples shown. For example, some embodiments cancombine, separate, add to, and/or omit components shown in FIG. 38 .Furthermore, the functionality of each of the components can be providedby one or more devices (e.g., computing devices) disposed in one or moregeographical locations.

Although the figures may refer to an “Epsilon Instrument,” “EpsilonHandheld Platform,” and specific remote services, various embodimentsthat fall within the scope of the invention are not so limited. Thetechniques described herein are described more generally and can beutilized by any variety of medical devices, mobile or other computingdevices, and remote servers. Moreover, specific software components andfunctionality described herein may be replaced withsimilarly-functioning software of various types. A person of ordinaryskill in the art will recognize some variations to the embodimentsillustrated herein and described below.

As illustrated in FIG. 38 , the diagnostic assay system can generallyinclude three types of components: a diagnostic device (the “EpsilonInstrument Hardware,” also referred to herein and in the figures as an“instrument” or “diagnostic device module” or “diagnostic device”), amobile device (the “Epsilon Handheld Platform”), and remote services(referring to the illustrated “Remote Xpert System” and “Remote Xpert+System” collectively). More detailed descriptions of these componentsare provided below. The diagnostic device and the mobile device can beco-located at a point of care, such as a health clinic, hospital, orother facility, while the remote services can be located at one or moreremote locations. Depending on desired functionality, and as indicatedabove, embodiments may employ multiple diagnostic devices, mobiledevices, and/or remote services.

Diagnostic device illustrated in FIG. 38 comprises the illustratedEpsilon Instrument Hardware and the various software componentsillustrated therein, including the Epsilon Instrument Core Software,Epsilon XpertReporter Software, Epsilon Instrument Interface Software,and Assay distributable. These components can communicate with eachother using various interfaces and application programming interfaces(APIs) as illustrated. As mentioned earlier, the diagnostic device cancomprise a diagnostic assay system having a combination of testing andcomputing components configured to conduct diagnostic assays and provideresulting data to remote services via the mobile device. In someembodiments, the diagnostic device may additionally process and/or storethe assay data from one or more assay results. Components may beimplemented, at least in part, using a combination of software andhardware, which can be incorporated into a computer system (such as thatdescribed in relation to FIG. 53 ).

In some embodiments, the diagnostic device can enable hands-offprocessing of patient samples (specimens) and provide both summarizedand detailed test results data to the remote services. Interfacesoftware (shown as the “Epsilon Instrument Interface Software”) canenable the diagnostic device to communicate with mobile device software(shown as the “Epsilon Handheld Software”) executed on the mobiledevice. Communication may be done wirelessly using any of a variety ofwireless technologies, such as near-field communication (NFC),Bluetooth™, Wi-Fi, and the like.

By establishing this communication with the mobile device, the interfacesoftware can thereby enable a user of the mobile device to controlvarious features of the diagnostic device. For example, using agraphical user interface (GUI) provided on a display of the mobiledevice, the user may be able to manage device settings of the diagnosticdevice; initiate, pause, or cancel tests conducted by the diagnosticdevice; specify the remote services to which the diagnostic device sendsdata; specify the type, content, and/or format of the data; and thelike. According to some embodiments, the mobile device may additionallyenable a user to access medical and/or other data stored on thediagnostic device. In some embodiments, however, the accessed data maynot be stored on the mobile device, thereby helping ensure that thesecurity of the data is not compromised if the mobile device is lost orstolen. This feature is advantageous helping the system meet and complywith various privacy laws, regulations and other standards.

The level of control provided to a user by the interface software viathe mobile device, may be dependent on a level of authorization providedby the user and/or mobile device. A user with a higher level ofauthorization can, for example, access features of the diagnostic deviceto which a user with a lower level of authorization does not haveaccess. The interface software may provide the authorization and/orauthentication of the user and/or mobile device prior to and/or duringcommunication by requiring, for example, login information or similarunique data to help ensure security of the system.

The diagnostic device may communicate with a plurality of mobiledevices, and may do so at the same time (or at substantially the sametime). As such, this can enable multiple users to control the diagnosticdevice. To do so, the interface software may provide authorizationand/or authentication for each of the plurality of mobile devices. Insome embodiments, where a diagnostic device is in active communicationwith a plurality of mobile devices, one of the mobile devices may bedesignated as the primary mobile device through which all data is sentto the remote services. In other words, in some embodiments, although adiagnostic device can be controlled by a plurality of mobile devices,the diagnostic device can also be tethered to a single, primary mobiledevice through which the diagnostic device routes data to the remoteservices.

The mobile device can comprise a mobile electronic device, such as asmartphone, tablet computer, laptop, and the like. The mobile devicesoftware can be executed as an application on the mobile device, and canfurther be agnostic of the operating system (OS) of the mobile device.As such, any of a wide variety of mobile devices can be able to functionas the mobile device described in embodiments herein once the mobiledevice software is installed on the mobile device and properauthentication is provided. As illustrated in FIG. 38 , the mobiledevice can also be connected with a printing device, such as anoff-the-shelf thermal printer.

In some embodiments, the mobile device software can enable authorizationand/or authentication of the mobile device with a plurality ofdiagnostic devices, such that a user can control a plurality ofdiagnostic devices at once with a single mobile device. In addition toproviding control of the diagnostic device via the mobile devicesoftware, the mobile device can further enable the diagnostic device tocommunicate with the remote services (e.g., provide data to the remoteservices) via a tethering feature that enables data communicated fromthe diagnostic device to the mobile device (e.g., via, NFC, Bluetooth,Wi-Fi, etc.) to be relayed to the remote services using the connectivityof the mobile device to a wide area network (WAN), which may utilizecellular (e.g., third generation (3G), long-term evolution (LTE), etc.),satellite, and/or other wireless technologies.

More generally, techniques described herein can provide for a diagnosticassay system in which one or more diagnostic assays can be controlledwith a mobile device using local area network (LAN)-based functionalityon a peer basis. That same protocol can be utilized for WANcommunication to remote services discretely on the mobile device. Thus,for this latter functionality, the mobile device can becomeself-contained router. Although embodiments described herein describethe use of a mobile or “handheld” device, other embodiments can utilizecomputing systems that may not be considered mobile or handheld, such asa personal computer. Features of the mobile device and other computingdevices described herein are described in more detail below in referenceto FIG. 53 .

According to some embodiments, the tethering feature can provideconnectivity between the diagnostic device and the remote serviceswithout any persistent data being stored on the mobile device. In otherwords, the mobile device may not know anything about the data that isbeing transferred. In some embodiments, for example, the mobile devicecan receive sensitive encrypted data, such as patient data, from thediagnostic device that is simply passed along to the remote reportingsystem without being stored or decrypted by the mobile device. In suchembodiments, the security of the data will therefore not be compromisedif the mobile device is lost or stolen, thereby adding another layer ofprivacy protection to the system which may help the system comply withgoverning privacy laws, regulations, or other standards. Moreover, thefunctionality of the diagnostic assay system can be restored in arelatively simple manner by replacing the lost or stolen mobile device.With such functionality, the techniques described herein can be utilizednot just in a laboratory, but also out in the field (e.g., an Ebolaclinic in a remote region in Africa) where a mobile device may be moresusceptible to loss or theft.

Referring again to FIG. 38 , the remote services can be executed in the“cloud” by one or more servers, which can be located at one or morelocations remote from the mobile device and/or diagnostic device. Theremote services can gather data from one or more diagnostic devices,synthesize the data, and store the data in a database. The remoteservices can gather data not only from one or more diagnostic devices ata single location (e.g., communicating via a particular mobile device),but also gather information more broadly from diagnostic devices atvarious facilities in various different geographical locations, therebybeing able to provide large-scale epidemiological data and determineother valuable health and disease information among one or morepopulations.

Additionally or alternatively, the remote services can aggregate andprocess data and provide a viewing entity (such as a governmentalagency) a secure portal (accessible, for example, via the Internet)through which the processed data can be accessed in various forms (e.g.,lists, graphs, geographic maps, and the like). The form by which theprocessed data is viewed is in accordance with the viewing entity'slevel of authorization. Again, the data sent to and processed by theremote services can be encrypted (or otherwise securely transferred)and/or manipulated in a manner that is compliant with laws, regulations,standards, and/or other applicable governing requirements.

It will be understood that components illustrated in FIG. 38 cancommunicate with each other using the wireless technologies mentionedabove either directly or as part of one or more larger datacommunication networks, such as the LAN and/or WAN described in theabove embodiments. The data communication network(s) can comprise anycombination of a variety of data communication systems, for example,cable, satellite, wireless/cellular, or Internet systems, or the like,utilizing various technologies and/or protocols, such as radio frequency(RF), optical, satellite, coaxial cable, Ethernet, cellular, twistedpair, other wired and wireless technologies, and the like. The datacommunication network(s) can comprise packet- and/or circuit-typeswitching, and can include one or more open, closed, public, and/orprivate networks, including the Internet, depending on desiredfunctionality, cost, security, and other factors.

The remaining description and figures illustrate various aspects of theembodiment of the diagnostic assay system illustrated in FIG. 38 .Although particular hardware and software components are described withrespect to the disclosed embodiment, a person of ordinary skill in theart will recognize that, in some embodiments, some such components canbe substituted, replaced, omitted, and/or otherwise altered as comparedto other embodiments. For example, programmable systems on a chip (PSoC)can be replaced with multiple components to provide substantially thesame functionality. A person of ordinary skill in the art will befamiliar with various mixed signal and/or analog microcontrollers thatare suitable for use with the invention. Representational State Transfer(REST) interfaces may be replaced and/or used in conjunction with othersoftware structures and/or protocols where appropriate, such as Create,Read, Update and Delete (CRUD); Domain Application Protocol (DAP);Hypermedia as the Engine of Application State (HATEOAS); Open DataProtocol (OData); RESTful API Modeling Language (RAML); RESTful ServiceDescription Language (RSDL); and the like.

IX. B. Epsilon Instrument Core Software

As illustrated in FIG. 38 , in some embodiments the Epsilon instrumentcore software (also referred to as diagnostic assay system software) caninclude a variety of software modules. Suitable modules that can beincluded in the instrument core software can include a Cellcoreoperating system module, a hardware state machine module (HSM), an iCOREsoftware module, a valve software module, a syringe/door softwaremodule, and/or an ultrasonic horn software module. In some embodiments,the Cellcore operating system module is a version of linux andsupporting services running on the Cellcore processor. In someembodiments, the HSM module can include all diagnostic device specificsoftware running on the Cellcore processor and outside of a Java VirtualMachine (JVM). In some embodiments, the iCore Software module includesall software running on the iCore PSoC. In some embodiments, the ValveSoftware module includes all software running on the Valve PSoC. In someembodiments, the Syringe/Door Software module includes all softwarerunning on the Syringe/Door PSoC. In some embodiments, the Horn Softwaremodule includes all software running on the Horn PSoC.

In some embodiments the Epsilon instrument interface software caninclude an Epsilon instrument REST interface module and an Epsilon AssayRunner Software module.

In some embodiments, the Epsilon Xpert Reporter Software operates as aclient of the Remote Xpert Software and runs on the Cellcore processorof the Epsilon instrument Hardware in the same JVM as the EpsilonInstrument Interface Software.

The Epsilon Instrument Hardware can be the physical subsystem thatperforms assays. In some embodiments, this subsystem may only includethe hardware of the instrument, with the software running on theinstrument as a separate subsystem.

IX. C. Mobile Device

As illustrated in FIG. 38 , in some embodiments the mobile device caninclude a variety of software modules. For example, embodiments of theillustrated Epsilon Handheld Software can comprise an Androidapplication, executed by the mobile device, specifically designed tosupport the system illustrated in FIG. 38 when deployed in the fieldcontext. In some embodiments, an application for another operatingsystem can be utilized. In some embodiments, the software can includeall of the necessary features to support performing tests on patients inthe field utilizing the diagnostic device, and/or features to facilitatethe Cepheid Service Department (or a service department of anotherprovider) remotely supporting these instruments.

In some embodiments, the mobile device can comprise an off-the-shelfAndroid handheld target platform, selected to support the field context.

IX. D. Remote Xpert+ System

In some embodiments, the Remote Xpert+ System illustrated in FIG. 38 cancomprise a collection of web applications exposed as services to be usedby Remote Xpert System and the Epsilon Handheld Software. REST and/orsimilar services (as previously described) can be used for internalcommunication within Remote Xpert+. In some embodiments, a limitednumber of services of the Remote Xpert+ System can be exposed toexternal systems, such as the Remote Xpert and Epsilon HandheldSoftware. According to some embodiments, a primary role of Remote Xpert+can be to allow central management of users, institutions, commands, andkits.

IX. E. Remote Xpert System

In some embodiments, the Remote Xpert System illustrated in FIG. 38 cancomprise a collection of web applications used by institutions to managetheir instruments and clinical data. Such institutions can include, forexample, national or international agencies (e.g., the World HealthOrganization), emergency response organizations, universities,hospitals, and the like. In some embodiments, the Remote Xpert softwarecan further include parsing software to parse incoming and/or outgoingdata.

IX. F. Assay Distributable

In some embodiments, components of an embodiment of the assaydistributable of the diagnostic device illustrated on FIG. 38 caninclude an assay header (summary information used to manage the assay),an assay definition (which can be, for example, a received file), and/orassay UI tailoring (which defines the assay specific UI such as specificsample preparation presentation instructions. Such tailoring can belimited to areas identified by the UI design, such as sample preparationsteps and/or assay specific help screens). In some embodiments, theassay distributable may optionally include assay specific software,which can allow the incorporation of new algorithms as needed for futureassays. This can require that the software executing assays supportsthis type of extension. Additionally, in some embodiments, the assaydistributable may include localized handheld assay resources, as needed.This can include various resources used to implement the UI for aspecific assay. Examples include localized strings for supportedlanguages, new graphic resources such as icons if any, and/or any helpfiles required (e.g. Portable Document Format (PDF) of the packageinsert or training videos). It can be further noted that, in someembodiments, the localized resources may need to be separated into an“assay language pack” or kit due to size constraints (e.g. localizedtraining videos) and regional variations.

IX. G. External Interfaces—Diagnostic Device

In some embodiments, the diagnostic device illustrated on FIG. 38 caninclude one or more external interfaces. For example, the EpsilonHandheld App GUI can be a user interface on the mobile device that actsas the user interface of the diagnostic device as well. The Remote XpertGUI can be a web-based user interface provided by Remote Xpert. TheRemote Xpert+GUI can be a web-based user interface provided by RemoteXpert+. In some embodiments, this GUI may be accessible only by theentity providing and/or maintaining the Remote Xpert+. Additionally oralternatively, external interfaces can include SMS messaging, which canbe used to report results to an institution clearing house, and can beprovided by the carrier via the mobile device operating system. Thediagnostic device can include a data streaming interface (the GXStreaming Data interface illustrated in FIG. 38 ) that enables apersonal computer (PC) or other computing device to provide avisualization of the data, which can aide in development and debugging.As such, this interface may not be used when deployed in the field, insome embodiments.

IX. H. Internal Interfaces—Diagnostic Device

In some embodiments, the diagnostic device illustrated on FIG. 38 caninclude one or more internal interfaces. For example, the EpsilonInstrument Hardware/Software interface can comprise an interface betweenthe instrument hardware and the Epsilon Instrument Core Software. TheGXIP+ interface can comprise an interface provided by the EpsilonInstrument Core Software and used by certain software in both theclinical setting context and in the field use context. The Assay RunnerInterface can be provided by the Epsilon Instrument Interface Softwareand used by the Epsilon Assay Runner Software or similar assay software.The Instrument Persistence API can comprise an interface provided by theEpsilon Instrument Interface Software and used by the Epsilon XpertReporter Software.

IX. I. Mobile Device Interfaces

In some embodiments, the mobile device can include a variety ofinterfaces. For example, the Epsilon Instrument Services interface cancomprise the primary interface provided by the Epsilon InstrumentInterface Software. For the field use context, this can be the interfaceused by the Epsilon Handheld Software to perform tests, get instrumentstatus updates, and other normal operations.

The Thermal Printer Interface can comprise an interface provided by theoptional thermal printer, which can be an off-the-shelf model with aWi-Fi network connection. This can enable the Epsilon Handheld Softwareto print tests results on the printer either automatically or at therequest of a user after a test result is available. In some embodiments,printers utilizing other technologies (e.g., ink, inkjet, etc.) can beused.

The Android Platform API can comprise interfaces provided by the AndroidOperating System used to access services of the mobile device hardwareand the network. As indicated previously, alternative embodiments mayinclude equivalent or similar components for alternative operatingsystems.

The coordination interface, which is illustrated in the embodiment ofFIG. 38 , provides for coordination between mobile devices when multiplemobile devices are simultaneously active at a particular location, whichmay happen at busy sites when more than one user is working or whenthere is a spare mobile that is active. The coordination interface canbe implemented to cross-connect all the modules to the user interfacefunctional control layer on the mobile device. The purposes andfunctions allow multiple instruments to be controlled and monitored viathe mobile device as autonomous units, and provide workflow coordinationbetween the devices for the operator to use the correct instruments forrunning a given diagnostic. Peer-to-peer, Wi-Fi-managed instruments canhave an assured specific control per device and maintain the chain ofcustody and critical patient identification parameters. The resultingfunctionality enables a X:Y ratio of mobile devices to diagnosticdevices, where X is any number of mobile devices, and Y is any number ofdiagnostic devices. In some embodiments, X and Y may be the same number.

IX. J. Remote Service Interfaces

As shown in FIG. 38 , the remote services can include variousinterfaces, in some embodiments. For example, the Epsilon Xpert ReporterInterface can comprise a collection of REST services that expose thefollowing capabilities: clinical data upload and/or instrumentsynchronization. The Remote Xpert+ Services Interface can comprisecollection of REST services that expose the following capabilities: kitmanagement, user management, institution & site management, remoteservice commands, and/or instrument synchronization.

IX. K. Clinical Laboratory Improvement Amendments (CLIA)-waivedApplications

In some embodiments, the core software interface of the diagnosticdevice of FIG. 38 can be utilized in a Clinical Laboratory ImprovementAmendments (CLIA)-waived application. Here, the diagnostic device canprovide information to proprietary software executed on a personalcomputer via an Ethernet connection. Alternative embodiments can employother computing hardware, software, and/or physical or wirelessconnections. Additional details regarding the GXIP+ interface areprovided below.

IX. L. Diagnostic Device—Software Components

FIG. 39 provides a logical view of software executed by the diagnosticdevice, according to an embodiment. As illustrated, the software caninclude low level drivers including the universal serial bus (USB)driver stack, SM Bus I/F, and Wi-Fi, Bluetooth, and USB dongle drivers.The application layer includes the operating system, as well as otherapplications. These applications can include a JVM having XpertReporterand Epsilon Rest Interface components, a JVM having an Epsilon AssayRunner component, a gateway application having a DX Gateway component,and/or an Epsilon Instrument Core application having GxIp+, GxStreaming, PSoC USB, HSM Layer, and Battery OF and Power Managementcomponents.

FIG. 40 is a block diagram of the Epsilon Instrument Core Architecture,according to some embodiments. The block diagram illustrates theinteraction of various subcomponents of the Epsilon Instrument CoreArchitecture including the NFC Interface, GxIp+ Interface, HSM. PSoCI/F, Gx Streaming interface, Xpert Reporter/Epsilon REST Interface,Epsilon Assay Runner, Dx Gateway, and NB USB, as described herein.

In some embodiments, the GxIp+ interface can be the primary componentsupporting the GxIp protocol and can implement the required Dx businesslogic. The business logic can be ported from 683xx legacy code as abasis for the “Northbound” instrument interface to ensure conformity inhow assays and commands are executed. In some embodiments, the GxIp+Interface can further contain the adaptive layer connecting the“Northbound” Legacy GxIp Commands and the “Southbound” Epsilon PSoCCommand interface. For the HBDC context, this can be the Dx equivalentinterface used by the Epsilon Instrument Interface Software to run andmonitor assays.

In some embodiments, the Gateway interface can be the componentsupporting the GxIp ‘Discovery’ protocol. Once discovery is complete,this component can act as a router for remote GxIp based components andthe GxIp+ interface. In some embodiments, the Gateway interface can bethe discovery interface on the Epsilon Instrument.

In some embodiments, the GxStreaming interface can be the primarycomponent supporting streaming of Epsilon Core state vectors to a remoteclient. During development this interface can be used to support theEngineering Visualization Tool (VT) for monitoring and tuning PSoCperformance, sonication and fluorimeter equivalence monitoring withrespect to the Legacy system. In some embodiments the GxStreaminginterface allows streaming of state swap data to the mobile device.

FIGS. 41-1 through 41-4 are diagrams illustrating various states of theHSM component, according to some embodiments. As used in thisdisclosure, the HSM can comprise the primary component managing the coreinstrument state as well as the legacy DX compatible sub-states.Additionally, the HSM can interact with the GxIp component to enable ordisable GxIp commands depending on the current instrument core state. Asillustrated in FIGS. 41-1 through 41-4 , high-level states can include,in some embodiments, POST—Power On Self Test, RECOVERY, IDLE,WAITING_FOR_CART, LOADING_CART, CARTRIDGE_LOADED, RUNNING_ASSAY,ABORTING, and CARTRIDGE_PRELOAD. It will be understood by a person ofordinary skill in the art that the names of these states are provided asnon-limiting examples, and names and functionality of such states canvary, depending on desired functionality.

FIG. 42 is a diagram illustrating instrument core internal componentsand interfaces, according to some embodiments. The PSoC USB, forexample, is an internal interface that can be a primary componentsupporting the “Southbound” interface to the PSoC Components (Horn,Door, Syringe, Valve, and ICORE). The component can use USB 2.0 tocreate a ‘data-backplane’ between the Cell Core and each PSOC. In someembodiments, during boot-up, PSoCs can be enumerated boot loadableendpoints, allowing new firmware to be programed on each PSoC. In someembodiments, during normal operations, PSoCs can be enumerated as acommand endpoint and a State Swap end point. Here, State Swap can affordhigh speed PSoC data virtualization on the Cell Core, allow monitoringand/or analysis of high speed PSoC data on the Cell Core, and/or supportthe Gx Streaming component on the Cell Core.

In some embodiments, instrument PSoC external interfaces can includeComms_Task, which can be a primary PSoC component supporting the“Southbound” interface between the PSoC and the Cell Core. It canfurther be a main component Pn the PSoC to create a “data-backplane”between the Cell Core and each PSoC. Additionally or alternatively, theComms_Task can be common to all PSoCs can create and manage the Commandand State Swap USB endpoint interface.

In some embodiments, the Analytics Task can comprise another PSoCexternal interface, which can be a primary PSoC component supporting thePSoCs command handling. In some embodiments, the Analytics Task caninclude common handling for common commands shared by all PSoCs.

Instrument PSoC external interfaces can further include ISRs, accordingto some embodiments of the invention. ISRs can allow for common handlingfor time on PSoCs, and/or specific priority processes for supportingbackground trajectory.

IX. M. Mobile Device—Software Components

FIG. 43 is a block diagram illustrating software components executed ona mobile device, according to some embodiments of the invention. Here,the User Interface can follow common Android (or other OS) designpatterns. Activities can be the components that control the flow throughthe user interface and which views are visible at any time. Views can bethe set of components that present information to the user. In someembodiments, most of the business logic can be contained in the ServicesComponents shown in FIG. 43 .

In some embodiments, the User Interface can present the specificworkflow required to run cartridge-based diagnostics on a standalonemodule and assure accuracy and granularity of patient data correlatedwith a specific diagnostic result. This includes automated chain ofcustody from sample logging through a cartridge and into the instrumentdatabase.

According to some embodiments, the Data Layer can include a Data Managerthat provides all database persistence in the application. In someembodiments, the Mobile Database can be SQLite and can be encryptedusing SQLCipher. The mobile database can include authorized users,credentials, and/or logging information. Because the mobile device canact as a self-contained mobile router for diagnostic data transport, thedata in the database can provide credentials and authentication toinitiate and terminate the transport connections. Additional informationregarding establishing these connections is provided below. In someembodiments, the Data Layer can further provide two API's to the rest ofthe system: a Data API for normal database objects, and a Logging APIfor logging key events. These APIs allow the mobile diagnostic device toconnect with the remote database and transparently move the diagnosticand other descriptive data via the mobile device from the diagnosticdevice to the contextually correct Internet instance of RemoteXpert.

As illustrated in FIG. 43 , embodiments may include a Site Manager,which manages the state of the site and can keep a list of known users,known diagnostic devices, known mobile devices, known assays, and/orknown printers. When the mobile device is connected to the internet, theSite Manager can coordinate with Remote Xpert+ to manage remote servicecommand for the site. The site manager can further interact with peermobile devices as necessary to manage site state, and/or handle userauthentication.

Some embodiments can further include a Cloud Communications, which canprovide access to the Remote Xpert+ Services, and/or a ConfigurationManager, which manages the current configuration of the mobile device.In other words, the Cloud Communications component can establish andmanage a bi-directional communication link with one or more remoteservices (e.g., the Remote Xpert+ as illustrated on FIG. 38 ). Thecommunications can be established via one or more APIs that can toparse, interpret, and transmit data (e.g., in a proprietary format) intoa standard readable format.

As further illustrated in FIG. 43 , embodiments may include anInstrument Manager, which manages the current list of instruments(medical diagnostic devices), and monitors the state of all theinstruments at the site. The Instrument Manager can further provide theability to perform operations on the diagnostic device(s). Suchoperations can include, for example, run a test using an assay, installan assay, install a software upgrade, perform diagnostics, and/orsynchronize time reference. The Instrument Manager can further select aninstrument when requesting a test and/or handle errors reported by aninstrument. According to some embodiments, the Instrument Communicationscan encapsulate the communication with the REST API of the medicaldiagnostic device.

Some embodiments may further include a Test Manager that can manage thelist of active tests, manage the workflow of performing a test, reportresults of the test after it is complete, and/or “archive” the test whenno longer active. In some embodiments, SMS Communications canencapsulate the reporting of results via SMS to an institutionalclearing house. In some embodiments, Printer Communications canencapsulate the ability to print reports on a local thermal printer.

Generally speaking, functionality of the mobile device can be dependenton available software development kits (SDKs) and APIs for variousplatforms. For example, for Android SDK and APIs, the applicationfunctionality is limited by the public APIs of the Android SDK. Even so,the Android SDK and APIs may be used to provide access to NFC, Camera,GPS, SMS Messaging, and/or the network.

Some embodiments may use SQLite and SQLCipher, which is the standarddatabase on Android. For instance, SQLCipher is referenced by the OpenWeb Application Security Project (OWASP) as the preferred way to securedata on the phone. Nonetheless alternative embodiments may utilize otherplatforms, such as iOS, Windows Mobile, and the like. Additionally oralternatively, other data structures and/or query languages may beutilized, such as SQL, HTSQL, jOOQ, and the like.

Some embodiments can provide for a third party remote supportapplication which enables remote display and, if available, remotecontrol of the mobile device provided by a third party application. Insome embodiments, versions of the mobile device software can use arelated SDK to provide remote control of the application.

Among other things, the invention provides for the consolidation of thecontrol of diagnostic device(s), management of the device(s), and LANand WAN connectivity functions (LAN to WAN routing, as previouslydescribed) on the mobile device, which are not employed by traditionalmedical diagnostic industry controls and communications. Thesegmentation of local control of the devices (the LAN layer) andcommunication with each of the diagnostic instruments can be done on apeer-to-peer level (e.g., via Wi-Fi) and manages the data flow for eachinstrument—both for the UI control functional interface and then thedata path interface up the RemoteXpert in the cloud.

The use of NFC on the mobile device, the NFC Adapter shown in FIG. 43 ,can be used to control chain of custody for patient samples. The medialdata provided to the claim can enable traceability of these functions,which can be stored in a central cloud repository. NFC can tie acartridge containing a patient sample simultaneously to a separate NFCsignal from the diagnostic device to assure matching for the custody andreporting accuracy requirements.

FIG. 43 further illustrates the instrument communications component,which can establish a peer-to-peer Wi-Fi connection between the mobiledevice and the diagnostic device. The instrument communicationscomponent can enable multiple mobile devices to communicate with oneanother. In some embodiments, the Handheld Coordinator can providecoordination among multiple mobile devices via Wi-Fi.

IX. N. Remote Diagnostics Reporting Service—Software Components

FIG. 44 is a block diagram illustrating software components executed bya remote diagnostics reporting service for medical diagnostics andepidemiology, according to some embodiments of the invention. The remotediagnostics reporting service comprises, among other things, a webserver, application server, database server, and file storage.

According to some embodiments, the logical components of the remotediagnostics reporting service illustrated in FIG. 44 can be described asfollows. The Remote Xpert+ Services can comprise REST web services to beused by the mobile device and Remote Xpert. The GUI Application cancomprise a web application to be used by an entity providing service andsupport to the diagnostic assay system. The Private Services cancomprise REST web services to be used by the GUI application. The CoreBusiness Logic Services can comprise REST web services containing allbusiness logic. The Audit and Logging Service can comprise REST webservices containing all logging and auditing capabilities. Finally, theFile Transfer Service can comprise a REST web service to abstract thefile storage solution.

Among other benefits, the diagnostics reporting service illustrated inFIG. 44 enables automated remote diagnostics reporting from a Class 2 orClass 3 medical diagnostic device into a remote database andpresentation layer. Additionally, layered authentication allows realtime remote control for debugging and diagnostics on a remote Class 2 orClass 3 medical diagnostic device across a WAN connection. This can be aservice consolidation of discrete functions including real timediagnostics and time series data specifically for application in a PCRbased diagnostic environment.

IX. O. Setup of a Diagnostic Assay System—Workflow

An example workflow for a setup of a molecular diagnostic assay systemsuch as the system shown on FIG. 38 can include the following stages. Itwill be understood that although specific wireless technologies (e.g.,GSM, CDMA, Wi-Fi, etc.) are mentioned in the example embodimentsprovided below, additional or alternative technologies may be used,depending on desired functionality.

First, mobile devices can be commissioned to work in the diagnosticassay system. Here, mobile devices utilize an internet connection (e.g.,a cellular connection, Wi-Fi, etc.). For cellar connections (e.g., GSM,CDMA, etc.), the mobile devices may need to be provisioned by a carrier.Additionally, mobile devices can be configured via Remote Xpert+, whichcan entail downloading an initial set of users, determining anauthorized set of assays, and being assigned to a site.

Second, the Wi-Fi Network can be configured. Here, a mobile device canbe selected to become Wi-Fi hotspot (e.g., the bridge between LAN andWAN networks), and other mobile devices can connect with the Wi-Fihotspot. In some embodiments, all diagnostic devices can use a singlemobile device acting as a Wi-Fi hotspot to access the Remote Xpertdirectly. Additionally or alternatively, one or more additional mobiledevices can connect via Wi-Fi to the mobile device acting as thehotspot. If the mobile device acting as the hotspot fails, runs out ofpower, or is lost, a second mobile device can be used in its place.

Third, the diagnostic devices can be configured. In some embodiments,this process can involve sharing Wi-Fi information (e.g., SSID andpassphrase) and/or other information with the mobile device. The mobiledevice can also get identifying information form the diagnostic devices,such as MAC address, serial number, etc. Such information sharing can beconducted using peer-to-peer NFC. Additional diagnostic devices can beadded in the manner above. If physical ordering is important, the UI ofthe mobile device can allow a user to specify where the new instrumentis to be placed.

IX. P. Data Flows of the Diagnostic Assay System

FIGS. 45-46 are data flow diagrams illustrating different aspects of adiagnostic assay system, according to some embodiments of the invention.As with other figures provided herein, FIGS. 45-46 are provided asnon-limiting examples. Alternative embodiments can include additionalfunctionality to that shown in the figure, and/or the functionalityshown in the figure may be omitted, combined, separated, and/orperformed simultaneously. Means for performing the functionality of theblocks may include one or more hardware and/or software components, suchas those shown in FIGS. 38 and 53 . A person of ordinary skill in theart will recognize some variations.

IX. Q. Diagnostic Assay System Top Level Data Flow

FIG. 45 is a data flow diagram illustrating top level data flow in adiagnostic assay system, such as the one illustrated in FIG. 38 . Here,the components of the diagnostic assay system—remote services, mobiledevice, and diagnostic device—are portrayed as circles, and data flow isportrayed as arrows.

The data flow can initiate with the mobile device sending the remoteservices a request for location configuration (1). The request can bemade when the mobile device is at a new site where the diagnostic deviceis located. As indicated in FIG. 45 , the request may only need to beperformed once per location.

The remote services then responds with location configuration (2), andthe remote services and mobile device exchange configuration description(3). As previously indicated, this involve downloading, from the remoteservices to the mobile device, an initial set of users, determining anauthorized set of assays, and more. The remote services can also provideoperational updates (4) to the mobile device.

The mobile device can then engage in a configuration process with thediagnostic device. In this process, the mobile device providesdiagnostic device registration (5) an operational updates (6) to thediagnostic device.

Once configured, the diagnostic device can receive operationalinstructions from the mobile device. The mobile device can then providedevice commands (7) to the diagnostic device, which may be based on userinput. As indicated previously, such commands can include, for example,run a test using an assay, install an assay, install a software upgrade,perform diagnostics, and/or synchronize time reference. The diagnosticdevice can provide command responses (8), such as acknowledgements,status updates, and the like.

Where device commands (7) result in executing medical diagnostics, thediagnostic device can then provide encrypted medical diagnostic results(9) to the remote services. As indicated previously, the mobile devicemay provide a hotspot through which the diagnostic device may send theencrypted medical diagnostic results (9). However, the mobile device maynot decrypt or store the data. As such, according to some embodiments,the mobile device acts simply as a conduit through which the encryptedmedical diagnostic results (9) can be reported to the remote services.In some embodiments, encrypted medical diagnostic results (10) can besent to the mobile device and stored. (As previously discussed, in someembodiments, the data may not be stored on the mobile device. In suchembodiments, the mobile device can send the data to another device—e.g.,a storage device on the LAN, a computer, etc.—for storage.) Depending ondesired functionality, the encrypted medical diagnostic results (10)sent to the mobile device may be the same or different than those sentto the remote services.

IX. R. Mobile Device Detailed Data Flow

FIG. 46 is a data flow diagram illustrating a more detailed data flow inwhich components of the mobile device—WAN interface component, medicaldiagnostic logic, and LAN interface component—are separately portrayed.

Similar to the flow of FIG. 45 , the flow shown in FIG. 46 can beginwith a configuration process between the mobile device and remoteservices. Here the medical diagnostic logic sends a request for locationconfiguration (1.1) to the WAN interface component, which then sends arequest for location configuration (1.2) to the remote services. Theremote services respond by providing location configuration (2.1) to theWAN interface component, which provides the location configuration (2.2)to the medical diagnostic logic. Configuration description is thenexchanged between the remote services and WAN interface component (3.1),the WAN interface component and medical diagnostic logic (3.2), medicaldiagnostic logic and LAN interface component (3.3), and LAN interfacecomponent and medical diagnostic device (3.4). Operational updates arethen passed from the remote services to the WAN interface component(4.1) and from the WAN interface component to the medical diagnosticlogic (4.2).

The diagnostic device configuration can include medical diagnosticdevice registration (5.1), (5.2), using the medical diagnostic logic,LAN interface component, and the device. These components further passoperational updates (6.1), (6.2) from the medical diagnostic logic tothe diagnostic device.

Device commands (7.1), (7.2) can then be sent from the medicaldiagnostic logic to the diagnostic device, and command responses (8.1),(8.2) can be sent back from the diagnostic device to the medicaldiagnostic logic.

Encrypted device results (9.1), (9.2) may be sent from the diagnosticdevice to the LAN interface component and then straight to the WANinterface component without passing through the medical diagnosticlogic. The encrypted diagnostic results (9.3) can then be sent to theremote services. As previously discussed, the encrypted diagnosticresults (10.1), (10.2) may be separately sent to a medical diagnosticlogic, which can then send them to an encrypted diagnostic results store(10.3). Depending on desired functionality, this store may be separatefrom the mobile device. Encrypted diagnostic results (11.1), (11.2) mayalso be sent from the medical diagnostic logic the remote services, viathe WAN interface component.

In some embodiments, the remote services may request a diagnostic. Asillustrated the remote services request a diagnostic (12.1), (12.2),(12.3), (12.4) which is relayed to the diagnostic device. This canprompt a diagnostic response (13.1), (13.2), (13.3), (13.4) that isrelayed back to the remote services.

IX. S. Work Flows of the Diagnostic Assay System

FIGS. 47-52 are flow charts illustrating the functions of differentaspects of a diagnostic assay system, such as the one illustrated inFIG. 38 , according to some embodiments of the invention. As with otherfigures provided herein, FIGS. 47-52 are provided as non-limitingexamples. Alternative embodiments may include additional functionalityto that shown in the figure, and/or the functionality shown in thefigure may be omitted, combined, separated, and/or performedsimultaneously. Means for performing the functionality of the blocks mayinclude one or more hardware and/or software components, such as thoseshown in FIGS. 38 AND 53 . A person of ordinary skill in the art willrecognize some variations.

IX. T. Location Configuration Network Work Flow

FIG. 47 is a data flow diagram illustrating the process for a locationconfiguration of a diagnostic assay system, according to an embodiment.Means for performing one or more blocks illustrated in FIG. 47 caninclude the remote services as described herein.

The process can start when a mobile device requests locationconfiguration. As previously explained, example data flows for such arequest are illustrated in FIGS. 45 and 46 . If the locationconfiguration is available, it is provided by the remote services. Ifnot, the remote services return an error.

IX. U. Operational Updates Network Work Flow—Mobile Device

FIG. 48 is a data flow diagram illustrating the process for providingoperational updates to a mobile device in a diagnostic assay system,according to some embodiments of the invention. Means for performing oneor more blocks illustrated in FIG. 48 can include the remote servicesand/or mobile device as described herein.

The process can start when a locally configured mobile device connectsto remote services. The remote services then obtain a description of themobile device operational description. If the description matches therequired mobile device configuration, the process can then end.Otherwise, the remote services send the mobile device an operationalconfiguration update.

IX. V. Operational Updates Network Work Flow—Diagnostic Device

FIG. 49 is a data flow diagram illustrating the process for providingoperational updates to a diagnostic device in a diagnostic assay system,according to some embodiments. Means for performing one or more blocksillustrated in FIG. 49 can include the mobile device and/or diagnosticdevice as described herein.

The process can start when the mobile device obtains a diagnostic deviceconfiguration description from the diagnostic device. If the diagnosticdevice configuration is correct, the process can end. Otherwise, themobile device can send an operational configuration update to thediagnostic device.

IX. W. Remote Diagnostics Network Work Flow

As discussed above in relation to FIG. 46 , remote services can requestdiagnostic information remotely. FIG. 50 is a data flow diagram of sucha process in a diagnostic assay system, according to an embodiment.Means for performing one or more blocks illustrated in FIG. 50 caninclude the remote services, mobile device, and/or diagnostic device asdescribed herein.

The process can start when remote services requests diagnosticinformation. The mobile device receives the diagnostic informationrequest. If the diagnostic request is for the mobile device, the mobiledevice will perform the requested mobile device diagnostic and send themobile device diagnostic information to the remote services. Otherwise,the diagnostic request is sent by the mobile device to the specifieddiagnostic device (which may be one of several at the site and/orcommunicatively linked with the mobile device). The diagnostic devicethen performs the requested diagnostics, and sends the diagnosticinformation to the mobile device. Finally, the mobile device sends thediagnostic device diagnostic information to the remote services.

IX. X. Medical Diagnostic Device Commands Network Work Flow

FIG. 51 is a data flow diagram illustrating the process for providingdiagnostic device commands in a diagnostic assay system, according tosome embodiments of the invention. Means for performing one or moreblocks illustrated in FIG. 51 can include the mobile device and/ordiagnostic device as described herein.

The process can start with the mobile device sending a command to adiagnostic device. The diagnostic device then processes the receivedcommand. Finally, the diagnostic device sends the response to the mobiledevice.

IX. Y. Diagnostic Device Registration Network Work Flow

FIG. 52 is a data flow diagram illustrating the process for providingdiagnostic device registration on a network of a diagnostic assaysystem, according to some embodiments of the invention. Means forperforming one or more blocks illustrated in FIG. 52 can include themobile device and/or diagnostic device as described herein.

The process can start when the mobile device queries the diagnosticdevice for device physical network identifier, such as a MAC address.The mobile device then provides network access information to thediagnostic device as previously described herein. Such information caninclude an SSID, username, and the like. In some embodiments, aspreviously described, the communication between the mobile device anddiagnostic device to this point may be via NFC and/or other wirelesstechnologies. The diagnostic device then connects to the network, andthe mobile device assigns a local identifier to the diagnostic device.

IX. Z. Computer System

FIG. 53 is an exemplary illustration of a computer system 5300, whichcan be incorporated, at least in part, into devices and components ofthe diagnostic assay system shown on FIG. 38 , including the diagnosticdevice (Epsilon Instrument), mobile device (Epsilon Handheld Platform),and/or or remote services (Remote Xpert System and Remote Xpert+System). FIG. 53 provides a schematic illustration of a computer system5300 that can perform the methods provided by various embodiments of theinvention. It should be noted that FIG. 53 is meant only to provide ageneralized illustration of various components, any or all of which canbe utilized as appropriate.

The computer system 5300 is shown comprising hardware elements that canbe electrically coupled via a bus 5306 (or may otherwise be incommunication, as appropriate). The hardware elements can include aprocessing unit, such as processor(s) 5310, which can include withoutlimitation one or more general-purpose processors, one or morespecial-purpose processors (such as digital signal processing chips,graphics acceleration processors, and/or the like), and/or otherprocessing means; one or more input devices 5315, which can includewithout limitation a mouse, a keyboard, a camera, a microphone, atouchscreen, medical testing hardware and/or diagnostic components,and/or the like; and one or more output devices 5320, which can includewithout limitation a display device, a printer, and/or the like.

The computer system 5300 can further include (and/or be in communicationwith) one or more non-transitory storage devices 5325, which cancomprise, without limitation, local and/or network accessible storage,and/or can include, without limitation, a disk drive, a drive array, anoptical storage device, a solid-state storage device, such as a randomaccess memory (“RAM”), and/or a read-only memory (“ROM”), which can beprogrammable, flash-updateable, and/or the like. Such storage devicescan be configured to implement any appropriate data stores, includingwithout limitation, various file systems, database structures, and/orthe like.

In some embodiments, the computer system 5300 can include acommunications subsystem 5330, which can include without limitation amodem, a network card (wireless or wired), an infrared communicationdevice, a wireless communication device, and/or a chipset (such as anNFC transceiver, a Bluetooth device, an 802.11 device, a Wi-Fi device, aWiMax device, cellular communication transceiver, etc.), and/or thelike. The communications subsystem 5330 can include one or more inputand/or output communication interfaces to permit data to be exchangedwith a network, other computer systems (e.g., using peer-to-peercommunication, as described herein), and/or any other electrical devicesdescribed herein. In some embodiments, the computer system 5300 willcomprise a working memory 5335, which can include a RAM or ROM device,as described above.

The computer system 5300 can comprise software elements, shown as beingcurrently located within the working memory 5335, including an operatingsystem 5340, device drivers, executable libraries, and/or other code,such as one or more application programs 5345, which can comprisecomputer programs provided by various embodiments (e.g., the mobiledevice software, interface software, etc.), and/or can be designed toimplement methods and/or software architecture, as described herein.Merely by way of example, methods and/or architecture provided in theother figures appended hereto, might be implemented as code and/orinstructions executable by a computer (and/or a processing unit within acomputer); in an aspect, then, such code and/or instructions can be usedto configure and/or adapt a general purpose computer (or other device)to perform one or more operations in accordance with the describedmethods.

A set of these instructions and/or code can be stored on anon-transitory computer-readable storage medium, such as the storagedevice(s) 5325 described above. In some embodiments, the storage mediumcan be incorporated within a computer system, such as computer system5300. In some embodiments, the storage medium can be separate from acomputer system (e.g., a removable medium, such as an optical disc),and/or provided in an installation package, such that the storage mediumcan be used to program, configure, and/or adapt a general purposecomputer with the instructions/code stored thereon. These instructionscan take the form of executable code, which is executable by thecomputer system 5300 and/or can take the form of source and/orinstallable code, which, upon compilation and/or installation on thecomputer system 5300 (e.g., using any of a variety of generallyavailable compilers, installation programs, compression/decompressionutilities, etc.), then takes the form of executable code.

It will be apparent to those skilled in the art that substantialvariations can be made in accordance with specific requirements. Forexample, customized hardware can be used, and/or particular elements canbe implemented in hardware, software (including portable software, suchas applets, etc.), or both. Connection to other computing devices suchas network input/output devices can be employed.

Some embodiments can employ a computer system (such as the computersystem 5300) to perform methods in accordance with some embodiments ofthe invention. In some embodiments, some or all of the procedures ofsuch methods are performed by the computer system 5300 in response toprocessor(s) 5310 executing one or more sequences of one or moreinstructions (which can be incorporated into the operating system 5340and/or other code, such as an application program 5345) contained in theworking memory 5335. Such instructions can be read into the workingmemory 5335 from another computer-readable medium, such as one or moreof the storage device(s) 5325. Merely by way of example, execution ofthe sequences of instructions contained in the working memory 5335 cancause the processor(s) 5310 to perform one or more procedures of themethods described herein. Additionally or alternatively, portions of themethods described herein can be executed through specialized hardware.

The terms “machine-readable storage medium” and “computer-readablestorage medium,” as used herein, refer to any storage medium thatparticipates in providing data that causes a machine to operate in aspecific fashion. In some embodiments implemented using the computersystem 5300, various computer-readable media can be involved inproviding instructions/code to processor(s) 5310 for execution and/orcan be used to store and/or carry such instructions/code. In someembodiments, a computer-readable storage medium is a physical and/ortangible storage medium. Such a medium can take the form of anon-volatile media or volatile media. Non-limiting examples ofnon-volatile media can include, optical and/or magnetic disks, such asthe storage device(s) 5325. Non-limiting examples of volatile media caninclude, without limitation, dynamic memory, such as the working memory5335.

Non-limiting common forms of physical and/or tangible computer-readablemedia can include, for example, a floppy disk, a flexible disk, harddisk, magnetic tape, or any other magnetic medium, a CD-ROM, any otheroptical medium, a RAM, a PROM, EPROM, a FLASH-EPROM, any other memorychip or cartridge, or any other medium from which a computer can readinstructions and/or code.

Various forms of computer-readable media can be involved in carrying oneor more sequences of one or more instructions to the processor(s) 5310for execution. Merely by way of example, the instructions may initiallybe carried on a magnetic disk and/or optical disc of a remote computer.A remote computer can load the instructions into its dynamic memory andsend the instructions as signals over a transmission medium to bereceived and/or executed by the computer system 5300.

The communications subsystem 5330 (and/or components thereof) generallywill receive signals, and the bus 5306 then can carry the signals(and/or the data, instructions, etc. carried by the signals) to theworking memory 5335, from which the processor(s) 110 retrieves andexecutes the instructions. The instructions received by the workingmemory 5335 can optionally be stored on a non-transitory storage device5325 either before or after execution by the processor(s) 5310.

IX. AA. Process Flow of Managing a Diagnostic Assay System

FIG. 54 is a flow diagram 5400 of a method of managing a diagnosticassay system with a mobile device, according to some embodiments of theinvention. As with other figures provided herein, FIG. 54 is provided asa non-limiting example. Some embodiments can include additionalfunctionality to that shown in the figure, and/or the functionalityshown in one or more of the blocks in the figure may be omitted,combined, separated, and/or performed simultaneously (or in closetemporal proximity). Means for performing the functionality of theblocks can include a mobile device as described herein, which canimplement one or more hardware and/or software components, such as thoseshown in FIG. 53 . A person of ordinary skill in the art will recognizesome variations that are suitable for use with the invention asdisclosed herein.

At block 5410, the mobile device receives user input for controlling thefunctionality of a diagnostic device. As described earlier, the mobiledevice can execute a software application providing a GUI with which auser can control various functions of the diagnostic device, such asmanage device settings of the diagnostic device; initiate, pause, orcancel medical tests conducted by the diagnostic device; specify theremote services to which the diagnostic device sends data; specify thetype, content, and/or format of the data; and the like. At block 5420,in response to receiving the user input, the mobile device sends controlinformation to the diagnostic device. If the mobile device iscommunicatively linked with a plurality of diagnostic devices, themobile device may first need to select or identify the diagnostic devicefrom the plurality of diagnostic devices.

At block 5430, the mobile device receives data from the diagnosticdevice. The data received may correspond to the type, content, and/orformat of the data specified at block 5410 (if such features werespecified). However, as indicated, the mobile device can act simply as apass-through device by which the diagnostic device can communicate witha remote server (e.g., one or more remote services as shown on FIG. 101). In other words, the mobile device can act as a transparent bridge,connecting a LAN (which may be peer-to-peer connected, as describedherein) to a WAN. But, as specified at block 5440, the received data canbe relayed to the server without storing or decrypting the data, therebyhelping ensure sensitive patient data is not compromised by the mobiledevice.

The methods, systems, and devices discussed above are examples. Variousconfigurations can omit, substitute, or add various procedures orcomponents as appropriate. For instance, in alternative configurations,the methods can be performed in an order different from that described,and/or various stages can be added, omitted, and/or combined. Also,features described with respect to certain configurations can becombined in various other configurations. Different aspects and elementsof the configurations can be combined in a similar manner. Also,technology evolves and some of the elements as described are provided asnon-limiting examples and thus do not limit the scope of the disclosureor claims.

Specific details are given in the description to provide a thoroughunderstanding of exemplary configurations (including implementations).However, configurations can be practiced without these specific details.For example, well-known circuits, processes, algorithms, structures, andtechniques have been shown without unnecessary detail in order to avoidobscuring the configurations. This description provides exemplaryconfigurations that do not limit the scope, applicability, orconfigurations of the claims. Rather, the preceding description of theconfigurations will provide those skilled in the art with an enablingdescription for implementing described techniques. Various changes canbe made in the function and arrangement of elements without departingfrom the spirit or scope of the disclosure.

Also, configurations can be described as a process which is depicted asa flow diagram or block diagram. Although each can describe theoperations as a sequential process, some of the operations can beperformed in parallel or concurrently. Furthermore, examples of themethods can be implemented by hardware, software, firmware, middleware,microcode, hardware description languages, or any combination thereof.When implemented in software, firmware, middleware, or microcode, theprogram code or code segments to perform the necessary tasks can bestored in a non-transitory computer-readable medium such as a storagemedium. Processors can perform the described tasks.

Terms, “and” and “or” as used herein, may include a variety of meaningsthat also is expected to depend at least in part upon the context inwhich such terms are used. Typically, “or” if used to associate a list,such as A, B, or C, is intended to mean A, B, and C, here used in theinclusive sense, as well as A, B, or C, here used in the exclusivesense. In addition, the term “one or more” as used herein may be used todescribe any feature, structure, or characteristic in the singular ormay be used to describe some combinations of features, structures, orcharacteristics. However, it should be noted that this is merely anillustrative example and claimed subject matter is not limited to thisexample. Furthermore, the term “at least one of” if used to associate alist, such as A, B, or C, can be interpreted to mean any combination ofA, B, and/or C, such as A, AB, AA, AAB, AABBCCC, etc.

Having described several exemplary configurations, variousmodifications, alternative constructions, and equivalents can be usedwithout departing from the spirit of the disclosure. For example, theabove elements can be components of a larger system, wherein other rulescan take precedence over or otherwise modify the application of theinvention. Also, a number of steps can be undertaken before, during, orafter the above elements are considered. Accordingly, the abovedescription does not bound the scope of the claims. All patents, patentapplications, and other publications cited in this application areincorporated by reference in their entirety for all purposes.

What is claimed is:
 1. A syringe drive sub-system for operating a syringe drive for a diagnostic assay system, comprising: a chassis of a diagnostic assay system; a brushless DC (BLDC) motor coupled to the chassis of a diagnostic assay system; a back drivable lead screw operable by the BLDC motor; a plunger rod operable by the lead screw to engage a removable assay cartridge, wherein the BLDC motor is configured to operate the lead screw based on monitoring current draw of the BLDC motor, the current being associated with pressure changes within the removable assay cartridge; and wherein the lead screw is not associated with any position sensors and the BLDC motor does not include any encoder hardware.
 2. The syringe drive sub-system of claim 1, wherein the plunger rod is coupled to the lead screw by a lateral arm.
 3. The syringe drive sub-system of claim 2, wherein the plunger rod is operable to engage with a plunger tip of the removable assay cartridge.
 4. The syringe drive sub-system of claim 1, wherein the BLDC motor is configured to alter operation to change pressure within the removable assay cartridge based on detecting the change in the current.
 5. The syringe drive sub-system of claim 4, wherein altering operation of the BLDC motor comprises raising the plunger rod to decrease pressure within the removable assay cartridge.
 6. The syringe drive sub-system of claim 4, wherein altering operation of the BLDC motor comprises lowering the plunger rod to increase pressure within the removable assay cartridge.
 7. The syringe drive sub-system of claim 4, wherein altering operation of the BLDC motor comprises decelerating the plunger rod to decrease pressure rate within the removable assay cartridge.
 8. The syringe drive sub-system of claim 4, wherein altering operation of the BLDC motor comprises accelerating the plunger rod to increase pressure rate within the removable assay cartridge.
 9. A method for operating a syringe drive for a diagnostic assay system, the method comprising: receiving a command to power a brushless DC (BLDC) motor, the BLDC motor operable to turn a back drivable lead screw, a plunger rod being coupled to and moveable by the lead screw; applying power to the BLDC motor to move the plunger rod to engage a plunger tip within a syringe passage of a removable assay cartridge; monitoring movement of the plunger rod within the syringe passage by monitoring at least one current associated with operation of the BLDC motor; detecting a change in the current of the BLDC motor; altering operation of the BLDC motor to effect change in the movement of the plunger rod within the removable assay cartridge based detecting the change in the current of the BLDC motor; and wherein the lead screw is not associated with any position sensors and the BLDC motor does not include any encoder hardware.
 10. The method of claim 9, wherein monitoring the at least one current of the BLDC motor occurs when the plunger rod is moving.
 11. The method of claim 10, wherein altering operation of the BLDC motor comprises raising the plunger rod to decrease pressure within the removable assay cartridge.
 12. The method of claim 10, wherein altering operation of the BLDC motor comprises lowering the plunger rod to increase pressure within the removable assay cartridge.
 13. The method of claim 10, wherein altering operation of the BLDC motor comprises decelerating the plunger rod to decrease pressure change rate within the removable assay cartridge.
 14. The method of claim 10, wherein altering operation of the BLDC motor comprises accelerating the plunger rod to increase pressure change rate within the removable assay cartridge. 